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{ "count": 7256, "next": "?page=2", "previous": null, "list": [ { "name": "vvv2_display", "description": "Display SNP proportions (vardict outputs), CDS (vadr annotations) of an assembly/genome, coverage depth (samtools depth), in png image and a tsv file, filtering results to summarize analyses (alignment, variant calling, annotation).", "homepage": "https://github.com/ANSES-Ploufragan/vvv2_display", "biotoolsID": "vvv2_display", "biotoolsCURIE": "biotools:vvv2_display", "version": [ "0.2.5.0" ], "otherID": [ { "value": "doi:10.3390/v17101385", "type": "doi", "version": "0.2.4.0" } ], "relation": [ { "biotoolsID": "ggplot2", "type": "uses" }, { "biotoolsID": "pysam", "type": "uses" }, { "biotoolsID": "R", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0287", "term": "Base position variability plotting" }, { "uri": "http://edamontology.org/operation_3184", "term": "Sequence assembly visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_3779", "term": "Annotated text" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "Inputs:\n- tbl pass vadr annotation file\n- tbl fail vadr annotation file\n- seqstat vadr output file\n- vcf vardict-java variant calling results (all)\n- samtools depth text file (coverage depth of an alignment)\nOutputs:\n- png summary file with all info\n- tsv file of indexed significant variant (index showed on png figure)\n- [optional] vcf file of significant variants only", "cmd": "vvv2_display.py -p vadr_pass_annotation.tbl -f vadr_fail_annotation.tbl -s vadr_seqstat.txt -n vardict-java_res.vcf -o samtools_depth_out.txt -r signif_snp_annot_res.png -u signif_snp_res.tsv -x signif_snp_res.vcf" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ANSES-Ploufragan/vvv2_display", "type": [ "Repository" ], "note": null }, { "url": "https://toolshed.g2.bx.psu.edu/view/ftouzain/vvv2_display/fcd3aa68bd39", "type": [ "Other" ], "note": "Galaxy wrapper" }, { "url": "https://workflowhub.eu/search?q=vvv2", "type": [ "Other" ], "note": "Listing of Galaxy workflow performing all steps:\n- alignment on ref/assembly\n- annotation of ref/assembly\n- coputation of coverage depth\n- vardict variant calling\n- vvv2_display synthesis\n\nOne can be found for each sequencing technology (Illumina SE/Proton, Illumina PE, nanopore, pacbio" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/v17101385", "pmid": "41157655", "pmcid": "PMC12567792", "type": [ "Primary" ], "version": "0.2.4.0", "note": "published in Viruses journal", "metadata": null } ], "credit": [ { "name": "Fabrice Touzain", "email": "fabrice.touzain@anses.fr", "url": "https://github.com/ANSES-Ploufragan/vvv2_display", "orcidid": "https://orcid.org/0000-0002-1103-2425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Dr. in Bioinformatics at ANSES (\"Swine virology, innovation and genomics\" Unit, Bioinformatics Team)" } ], "owner": "fabrice", "additionDate": "2026-02-12T16:06:53.794717Z", "lastUpdate": "2026-02-12T16:07:53.280544Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Metagenomic operational taxonomic units (mOTUs)", "description": "Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. 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HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maria Beser-Robles", "email": "maria_beser@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-0072-5525", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T12:09:16.704255Z", "lastUpdate": "2026-02-03T11:47:01.186875Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)", "description": "The tool performs an automatic segmentation of the possible DIPG tumours on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W and Flair/T2-weighted magnetic resonance images. The tool includes a complete workflow from DICOM images to DICOM seg tumoral masks.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_dipg_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_dipg_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input -v /path/to/output:/output harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest \\\n --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\":\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"}}'" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://link.springer.com/article/10.1007/s10278-025-01557-9", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-025-01557-9", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - 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It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.\n\nTRAINING & VALIDATION COHORTS:\n\nInitial Development (Veiga-Canuto 2022):\n-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).\n-Internal validation: 26 patients (median DSC 0.918 ± 0.067).\n-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).\n-Mean age: 37.6 ± 39.3 months.\n-Median tumor volume: 116,518 mm³.\n\nExternal Validation (Veiga-Canuto 2023):\n-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).\n-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.\n-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).\n-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": "docker run --rm \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n --gpus all \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n --mode dicom-seg \\\n --series-selector /output/config/series_to_segment.csv \\\n --seg-series-number 2302001 \\\n --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\" \\\n --seg-coordinating-center \"EUCAIM Consortium\" \\\n --keep-nifti false" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.mdpi.com/2072-6694/14/15/3648", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.3390/cancers14153648", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.3390/cancers15051622", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Diana Veiga Canuto", "email": "dianaveigac@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6048-2940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Support", "Documentor", "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support", "Documentor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T09:08:44.174795Z", "lastUpdate": "2026-02-03T11:40:55.741817Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "jmztab-m", "description": "Reference implementation for mzTab 2.0 for metabolomics", "homepage": "https://github.com/lifs-tools/jmzTab-m", "biotoolsID": "jmztab-m", "biotoolsCURIE": "biotools:jmztab-m", "version": [ "0.9.6", "1.0.1", "1.0.2", "1.0.4", "1.0.5", "1.0.6" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "Apache-2.0", "collectionID": [ "de.NBI" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/lifs-tools/jmzTab-m", "type": [ "Repository" ], "note": null }, { "url": "https://anaconda.org/bioconda/jmztab-m", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/lifs-tools/jmzTab-m/releases", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/lifs-tools/jmzTab-m/blob/master/README.adoc", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.analchem.9b01987", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "1.0.4", "note": null, "metadata": null } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/lifs-tools/jmzTab-m", "orcidid": "https://orcid.org/0000-0002-6540-6875", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "de.NBI_Service_Team", "additionDate": "2018-06-21T08:37:35Z", "lastUpdate": "2026-02-03T10:26:12.147063Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "decompTumor2Sig", "description": "R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.", "homepage": "http://rmpiro.net/decompTumor2Sig/", "biotoolsID": "decompTumor2Sig", "biotoolsCURIE": "biotools:decompTumor2Sig", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/rmpiro/decompTumor2Sig", "type": [ "Repository" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://rmpiro.net/index.html#downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-019-2688-6", "pmid": "30999866", "pmcid": "PMC6472187", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DecompTumor2Sig: Identification of mutational signatures active in individual tumors", "abstract": "© 2019 The Author(s).Background: The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic processes like age-related spontaneous deamination of 5-methylcytosine. The effect of such mutational processes can be modeled by mutational signatures, of which two different conceptualizations exist: the model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial identification and definition of mutational signatures requires large sets of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use R package that can decompose an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor. Until now, such tools were available only for Alexandrov signatures. We demonstrate the correctness and usefulness of our approach with three test cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor genomes of ten different tumor entities, and from simulated tumor genomes, respectively. Conclusions: The decompTumor2Sig package is freely available and has been accepted for inclusion in Bioconductor.", "date": "2019-04-18T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Kruger S." }, { "name": "Piro R.M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Prof. Dr. Rosario M. Piro", "email": "r.piro@fu-berlin.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "Ruta", "additionDate": "2019-06-20T14:18:28Z", "lastUpdate": "2026-02-02T08:12:42.981321Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-POLIMI" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DrugComb", "description": "The data portal for drug combination and monotherapy sensitivity screenings.\n[v1.5] DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. https://doi.org/10.1093/nar/gkab438\n[v1.4] DrugComb: an integrative cancer drug combination data portal. https://doi.org/10.1093/nar/gkz337", "homepage": "https://researchportal.helsinki.fi/en/datasets/drugcomb/", "biotoolsID": "DrugComb", "biotoolsCURIE": "biotools:DrugComb", "version": [ "1.5" ], "otherID": [], "relation": [ { "biotoolsID": "synergyfinder", "type": "uses" } ], "function": [], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [], "license": "Unlicense", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://researchportal.helsinki.fi/en/datasets/drugcomb/", "type": [ "Repository" ], "note": "alternative links" }, { "url": "https://twitter.com/DrugComb", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/11102665", "type": "Downloads page", "note": "https://zenodo.org/records/11102665", "version": "1.4 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"gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jtang920", "additionDate": "2019-08-09T13:06:36Z", "lastUpdate": "2026-02-01T17:44:46.966665Z", "editPermission": { "type": "group", "authors": [ "jtang920" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pantas", "description": "Differential quantification of alternative splicing events on spliced pangenome graphs.", "homepage": "https://github.com/algolab/pantas", "biotoolsID": "pantas", "biotoolsCURIE": "biotools:pantas", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/AlgoLab/pantas", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/AlgoLab/pantas/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/AlgoLab/pantas", "type": "Source code", "note": null, "version": null }, { "url": "https://hub.docker.com/r/algolab/pantas", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/AlgoLab/pantas/blob/main/README.md", "type": [ "General", "Installation instructions", "Quick start guide", "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1012665", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "yp", "additionDate": "2026-01-30T22:36:14.902508Z", "lastUpdate": "2026-01-30T22:36:14.904749Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RecGraph", "description": "RecGraph is a tool for computing optimal sequence-to-graph alignment with recombinations.", "homepage": "https://github.com/AlgoLab/RecGraph", "biotoolsID": "recgraph", "biotoolsCURIE": "biotools:recgraph", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3796", "term": "Population genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Rust" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": null, "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/AlgoLab/RecGraph", "type": [ "Repository" ], "note": null }, { "url": 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Based on interaction geometries previously derived from protein crystal structures potential water positions are generated for free interaction directions (lone pairs of acceptors or hydrogen atoms of donors). Every small molecule present in the PDB structure is used to generate an active site of 6.5 Å radius around each atom. Within these active sites water molecules are placed.\nIn the corresponding publication we showed that WarPP is able to place 80% of water molecules within 1.0 Å distance to a crystallographically observed one.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#warpp", "biotoolsID": "warpp", "biotoolsCURIE": "biotools:warpp", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jcim.8b00271", "pmid": "30036062", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples", "abstract": "Water molecules are of great importance for the correct representation of ligand binding interactions. Throughout the last years, water molecules and their integration into drug design strategies have received increasing attention. Nowadays a variety of tools are available to place and score water molecules. However, the most frequently applied software solutions require substantial computational resources. In addition, none of the existing methods has been rigorously evaluated on the basis of a large number of diverse protein complexes. Therefore, we present a novel method for placing water molecules, called WarPP, based on interaction geometries previously derived from protein crystal structures. Using a large, previously compiled, high-quality validation set of almost 1500 protein-ligand complexes containing almost 20000 crystallographically observed water molecules in their active sites, we validated our placement strategy. We correctly placed 80% of the water molecules within 1.0 Å of a crystallographically observed one.", "date": "2018-08-27T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Nittinger E." }, { "name": "Flachsenberg F." }, { "name": "Bietz S." }, { "name": "Lange G." }, { "name": "Klein R." }, { "name": "Rarey M." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "ehrt", "additionDate": "2020-06-08T16:17:43Z", "lastUpdate": "2025-12-23T14:50:38.010415Z", "editPermission": { "type": "group", "authors": [ "ehrt" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "StructureProfiler", "description": "Tool for 3D protein structure profiling.", "homepage": "https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html", "biotoolsID": "StructureProfiler", "biotoolsCURIE": "biotools:StructureProfiler", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0249", "term": "Protein geometry calculation" }, { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" }, { "uri": "http://edamontology.org/operation_0482", "term": "Protein-ligand docking" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://software.zbh.uni-hamburg.de/pages/getPackage", "type": "Downloads page", "note": "NAOMI ChemBio Suite including the package", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/bty692", "pmid": "30124779", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "StructureProfiler: An all-in-one tool for 3D protein structure profiling", "abstract": "Motivation Three-dimensional protein structures are important starting points for elucidating protein function and applications like drug design. Computational methods in this area rely on high quality validation datasets which are usually manually assembled. Due to the increase in published structures as well as the increasing demand for specially tailored validation datasets, automatic procedures should be adopted. Results StructureProfiler is a new tool for automatic, objective and customizable profiling of X-ray protein structures based on the most frequently applied selection criteria currently in use to assemble benchmark datasets. As examples, four dataset configurations (Astex, Iridium, Platinum, combined), all results of the combined tests and the list of all PDB Ids passing the combined criteria set are attached in theSupplementary Material.", "date": "2019-03-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Meyder A." }, { "name": "Kampen S." }, { "name": "Sieg J." }, { "name": "Fahrrolfes R." }, { "name": "Friedrich N.-O." }, { "name": "Flachsenberg F." }, { "name": "Rarey M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Matthias Rarey", "email": "rarey@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2019-07-06T06:35:25Z", "lastUpdate": "2025-12-23T14:50:37.487104Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "StructureProfiler", "description": "StructureProfiler was developed as an all-in-one tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods. Test configurations based on either the Astex, the Iridium HT, the Platinum, or the combination of all three criteria catalogs. (Note that RSCC as an electron density validation criteria was replaced by EDIAm scoring).", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#structureprofiler", "biotoolsID": "structurechecker", "biotoolsCURIE": "biotools:structurechecker", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2087", "term": "Molecular property" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty692", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "StructureProfiler: An all-in-one tool for 3D protein structure profiling", "abstract": "© The Author(s) 2018.Motivation Three-dimensional protein structures are important starting points for elucidating protein function and applications like drug design. Computational methods in this area rely on high quality validation datasets which are usually manually assembled. Due to the increase in published structures as well as the increasing demand for specially tailored validation datasets, automatic procedures should be adopted. Results StructureProfiler is a new tool for automatic, objective and customizable profiling of X-ray protein structures based on the most frequently applied selection criteria currently in use to assemble benchmark datasets. As examples, four dataset configurations (Astex, Iridium, Platinum, combined), all results of the combined tests and the list of all PDB Ids passing the combined criteria set are attached in theSupplementary Material.", "date": "2019-03-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Meyder A." }, { "name": "Kampen S." }, { "name": "Sieg J." }, { "name": "Fahrrolfes R." }, { "name": "Friedrich N.-O." }, { "name": "Flachsenberg F." }, { "name": "Rarey M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "ehrt", "additionDate": "2020-06-08T18:35:57Z", "lastUpdate": "2025-12-23T14:50:36.983259Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protoss", "description": "Fully automated hydrogen prediction tool for protein-ligand complexes. It adds missing hydrogen atoms to protein structures and detects reasonable protonation states, tautomers, and hydrogen coordinates of both protein and ligand molecules. It investigates hydrogen bonds, metal interactions and repulsive atom contacts for all possible states and calculates an optimal hydrogen bonding network within these degrees of freedom.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#protoss", "biotoolsID": "protoss", "biotoolsCURIE": "biotools:protoss", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0394", "term": "Hydrogen bond calculation" }, { "uri": "http://edamontology.org/operation_2949", "term": "Protein interaction analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI", "COVID-19" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1758-2946-6-12", "pmid": "24694216", "pmcid": "PMC4019353", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Protoss: A holistic approach to predict tautomers and protonation states in protein-ligand complexes", "abstract": "The calculation of hydrogen positions is a common preprocessing step when working with crystal structures of protein-ligand complexes. An explicit description of hydrogen atoms is generally needed in order to analyze the binding mode of particular ligands or to calculate the associated binding energies. Due to the large number of degrees of freedom resulting from different chemical moieties and the high degree of mutual dependence this problem is anything but trivial. In addition to an efficient algorithm to take care of the complexity resulting from complicated hydrogen bonding networks, a robust chemical model is needed to describe effects such as tautomerism and ionization consistently. We present a novel method for the placement of hydrogen coordinates in protein-ligand complexes which takes tautomers and protonation states of both protein and ligand into account. Our method generates the most probable hydrogen positions on the basis of an optimal hydrogen bonding network using an empirical scoring function. The high quality of our results could be verified by comparison to the manually adjusted Astex diverse set and a remarkably low rate of undesirable hydrogen contacts compared to other tools. © 2014 Bietz et al.; licensee Chemistry Central Ltd.", "date": "2014-04-03T00:00:00Z", "citationCount": 153, "authors": [ { "name": "Bietz S." }, { "name": "Urbaczek S." }, { "name": "Schulz B." }, { "name": "Rarey M." } ], "journal": "Journal of Cheminformatics" } }, { "doi": "10.1186/1758-2946-1-13", "pmid": "20298519", "pmcid": "PMC3225823", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Fast automated placement of polar hydrogen atoms in protein-ligand complexes", "abstract": "Background. Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results. We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion. Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation. © 2009 Lippert and Rarey; licensee BioMed Central Ltd.", "date": "2009-12-01T00:00:00Z", "citationCount": 58, "authors": [ { "name": "Lippert T." }, { "name": "Rarey M." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "rarey-office@zbh.uni-hambugr.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2016-11-28T10:07:16Z", "lastUpdate": "2025-12-23T14:50:36.482733Z", "editPermission": { "type": "group", "authors": [ "Bietz", "ehrt" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PoseView", "description": "This tool automatically creates two-dimensional diagrams which depict the protein-ligand interactions and conform to chemical drawing conventions. Directed interactions between protein and ligand are estimated by an integrated scoring scheme and depicted as lines between detailed structure diagrams for both protein residues and the ligand molecule.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#poseview", "biotoolsID": "poseview", "biotoolsCURIE": "biotools:poseview", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btl150", "pmid": "16632493", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Molecular complexes at a glance: Automated generation of two-dimensional complex diagrams", "abstract": "Motivation: In this paper a new algorithmic approach is presented, which automatically generates structure diagrams of molecular complexes. A complex diagram contains the ligand, the amino acids of the protein interacting with the ligand and the hydrophilic interactions schematized as dashed lines between the corresponding atoms. The algorithm is based on a combinatorial optimization strategy which solves parts of the layout problem non-heuristically. The depicted molecules are represented as structure diagrams according to the chemical nomenclature. Due to the frequent usage of complex diagrams in the scientific literature as well as in text books dealing with structural biology, biochemistry and medicinal chemistry, the new algorithm is a key element for computer applications in these areas. Results: The method was implemented in the new software tool PoseView. It was tested on a representative dataset containing 305 protein - ligand complexes in total from the Brookhaven Protein Data Bank. PoseView was able to find collision-free layouts for more than three quarters of all complexes. In the following the layout generation algorithm is presented and, additional to the statistical results, representative test cases demonstrating the challenges of the layout generation will be discussed. © 2006 Oxford University Press.", "date": "2006-07-15T00:00:00Z", "citationCount": 349, "authors": [ { "name": "Stierand K." }, { "name": "Maass P.C." }, { "name": "Rarey M." } ], "journal": "Bioinformatics" } }, { "doi": "10.1002/cmdc.200700010", "pmid": "17436259", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "From modeling to medicinal chemistry: Automatic generation oft wo-dimensional complex diagrams", "abstract": "As a result of the increasing application of structure-based drug design, the visualization of protein-ligand complexes has become an important feature in medicinal chemistry. The large number of experimentally resolved complex structures and the further development of computer-aided methods like docking or de novo design establishes new possibilities in this field. During lead finding and optimization, a manual investigation of many complexes and their interaction patterns is typically performed. We present an algorithm that automatically generates 2D-protein-ligand diagrams as a possible solution for a transparent visualization of the contact partners in a complex and as a support for scientists in the evaluation of structure-based design results. Running the software on representative test data sets, it generates collision free layouts for ∼76% of the cases in the range of tenths of a second per complex. The success rate for complexes with ligands which have a molecular weight >500 Da is 87 %. © 2007 Wiley-VCH Verlag GmbH & Co. KGaA.", "date": "2007-06-11T00:00:00Z", "citationCount": 84, "authors": [ { "name": "Stierand K." }, { "name": "Rarey M." } ], "journal": "ChemMedChem" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "rarey-office@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2016-11-21T10:33:07Z", "lastUpdate": "2025-12-23T14:50:36.016352Z", "editPermission": { "type": "group", "authors": [ "Bietz", "ehrt" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HyPPI", "description": "HyPPI classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact. Permanent protein-protein complexes are only stable in their complexed state and the subunits would denature upon complex dissociation. Transient protein-protein complexes are stable in the complexed form as well as in the monomeric depending of the necessary function of the complex. Crystal artifacts have no biological function and are artifically formed during crystallization process. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface (ΔGHydrophobic) and the quotient of interface area ratios (IF-quotient). The IF-quotient takes the symmetry of the protein-protein interface into account.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#ppi", "biotoolsID": "ppi", "biotoolsCURIE": "biotools:ppi", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": "Probability score for interface classification", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s10822-012-9626-2", "pmid": "23269578", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: Methods behind the HYDE scoring function", "abstract": "The estimation of free energy of binding is a key problem in structure-based design. We developed the scoring function HYDE based on a consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes. HYDE is applicable to all types of protein targets since it is not calibrated on experimental binding affinity data or protein-ligand complexes. The comprehensible atom-based score of HYDE is visualized by applying a very intuitive coloring scheme, thereby facilitating the analysis of protein-ligand complexes in the lead optimization process. In this paper, we have revised several aspects of the former version of HYDE which was described in detail previously. The revised HYDE version was already validated in large-scale redocking and screening experiments which were performed in the course of the Docking and Scoring Symposium at 241st ACS National Meeting. In this study, we additionally evaluate the ability of the revised HYDE version to predict binding affinities. On the PDBbind 2007 coreset, HYDE achieves a correlation coefficient of 0.62 between the experimental binding constants and the predicted binding energy, performing second best on this dataset compared to 17 other well-established scoring functions. Further, we show that the performance of HYDE in large-scale redocking and virtual screening experiments on the Astex diverse set and the DUD dataset respectively, is comparable to the best methods in this field. © 2012 Springer Science+Business Media Dordrecht.", "date": "2013-01-01T00:00:00Z", "citationCount": 218, "authors": [ { "name": "Schneider N." }, { "name": "Lange G." }, { "name": "Hindle S." }, { "name": "Klein R." }, { "name": "Rarey M." } ], "journal": "Journal of Computer-Aided Molecular Design" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "rarey-office@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2016-11-28T10:07:16Z", "lastUpdate": "2025-12-23T14:50:31.665805Z", "editPermission": { "type": "group", "authors": [ "ehrt" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EDIA", "description": "Easily interpretable electron density score for individual atoms. It quantifies the electron density support of each single atom by computing a weighted sum over an oversampled electron density grid in the proximity of the atom. Atomic EDIA values can also be combined with the help of the power mean to compute EDIA_m, an electron density score for small molecules, fragments, or residues.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#edia", "biotoolsID": "edia", "biotoolsCURIE": "biotools:edia", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0321", "term": "Protein model validation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": "Score for structure quality assessment on a global or atomistic level", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_2828", "term": "X-ray diffraction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI", "COVID-19" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jcim.7b00391", "pmid": "28981269", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures", "abstract": "© 2017 American Chemical Society.Macromolecular structures resolved by X-ray crystallography are essential for life science research. While some methods exist to automatically quantify the quality of the electron density fit, none of them is without flaws. Especially the question of how well individual parts like atoms, small fragments, or molecules are supported by electron density is difficult to quantify. While taking experimental uncertainties correctly into account, they do not offer an answer on how reliable an individual atom position is. A rapid quantification of this atomic position reliability would be highly valuable in structure-based molecular design. To overcome this limitation, we introduce the electron density score EDIA for individual atoms and molecular fragments. EDIA assesses rapidly, automatically, and intuitively the fit of individual as well as multiple atoms (EDIAm) into electron density accompanied by an integrated error analysis. The computation is based on the standard 2fo - fc electron density map in combination with the model of the molecular structure. For evaluating partial structures, EDIAm shows significant advantages compared to the real-space R correlation coefficient (RSCC) and the real-space difference density Z score (RSZD) from the molecular modeler's point of view. Thus, EDIA abolishes the time-consuming step of visually inspecting the electron density during structure selection and curation. It supports daily modeling tasks of medicinal and computational chemists and enables a fully automated assembly of large-scale, high-quality structure data sets. Furthermore, EDIA scores can be applied for model validation and method development in computer-aided molecular design. 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