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{ "count": 33011, "next": "?page=2", "previous": null, "list": [ { "name": "PrimerPickr", "description": "Primerpickr is an open-source tool for rational primer design powered by the aggregation of public usage of pcr primers", "homepage": "https://www.primerpickr.com", "biotoolsID": "primerpickr", "biotoolsCURIE": "biotools:primerpickr", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [], "operatingSystem": [], "language": [], "license": "CC-BY-NC-ND-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "thomas1", "additionDate": "2026-05-16T23:32:20.372457Z", "lastUpdate": "2026-05-16T23:34:00.964442Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HyPPI", "description": "HyPPI classifies a protein-protein complex based on its interaction type into permanent, transient, or crystal artifact. Permanent protein-protein complexes are only stable in their complexed state. Their subunits would denature upon dissociation of the protein-protein complex. Transient protein-protein complexes are stable in the complexed as well as in the monomeric form, depending on the necessary function of the complex. Crystal artifacts have no biological function and are artificially formed during the 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). 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Multiple EDIA values can be combined using the power mean to compute the EDIAm, i.e., the electron density score for a group of several atoms. It enables users to score a set of atoms, such as a ligand, a residue, or an active site.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.html", "biotoolsID": "edia", "biotoolsCURIE": "biotools:edia", "version": [], "otherID": [], "relation": [ { "biotoolsID": "structureprofiler", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" } ], "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" }, { "uri": "http://edamontology.org/format_3814", "term": "SDF" } ] } ], "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" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Score for structure quality assessment on a global or atomistic level", "cmd": null } ], "toolType": [ "Web service", "Command-line tool", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_2828", "term": "X-ray diffraction" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://proteins.plus", "type": [ "Service" ], "note": "A web service to run EDIAscorer calculations for protein structures stored in the Protein Data Bank." }, { "url": "https://proteins.plus/help/edia_rest", "type": [ "Service" ], "note": "A web API to run EDIAscorer calculations for protein structures stored in the Protein Data Bank." }, { "url": "https://uhh.de/naomi", "type": [ "Software catalogue" ], "note": "A link to download the standalone tool from the NAOMI ChemBio Suite." } ], "download": [ { "url": "https://uhh.de/naomi", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://proteins.plus/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jcim.7b00391", "pmid": "28981269", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "ProteinsPlus Support", "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "NAOMI ChemBio Suite Support", "email": "software.zbh@uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": null, "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2016-11-28T10:07:17Z", "lastUpdate": "2026-05-16T15:37:23.257129Z", "editPermission": { "type": "group", "authors": [ "ehrt", "MelanieZBH" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "StructureProfiler", "description": "Three-dimensional protein structures play a vital role in drug design. 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Published by Oxford University Press on behalf of Nucleic Acids Research.The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio.", "date": "2016-07-08T00:00:00Z", "citationCount": 213, "authors": [ { "name": "Blom J." }, { "name": "Kreis J." }, { "name": "Spanig S." }, { "name": "Juhre T." }, { "name": "Bertelli C." }, { "name": "Ernst C." }, { "name": "Goesmann A." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "bigi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://edgar.computational.bio", "orcidid": "http://orcid.org/0000-0001-6455-3622", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Jochen Blom", "email": "jochen.blom@computational.bio.uni-giessen.de", "url": null, "orcidid": "http://orcid.org/0000-0001-6455-3622", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "linJW", "additionDate": "2018-08-09T13:02:10Z", "lastUpdate": "2026-05-13T09:23:14.609265Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CPMCP", "description": "A database of Chinese patent medicine and compound prescription.", "homepage": "http://cpmcp.top", "biotoolsID": "cpmcp", "biotoolsCURIE": "biotools:cpmcp", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_3373", "term": "Drug development" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/DATABASE/BAAC073", "pmid": "36006844", "pmcid": "PMC9408024", "type": [], "version": null, "note": null, "metadata": { "title": "CPMCP: a database of Chinese patent medicine and compound prescription", "abstract": "© The Author(s) 2022. Published by Oxford University Press.Although several traditional Chinese medicine (TCM)-related databases have emerged, they focus on researching single medicinal materials, which is far from sufficient for clinical research and application. In comparison, compound prescriptions are more informative and meaningful in TCM, for they embody the information on the compatibility of TCM besides the relatively isolated information about single medicinal materials. The compatibility information is essential in TCM because it conveys not only what components are involved to treat special diseases but also how to combine these single medical materials. We established a database of Chinese patent medicine and compound prescription (CPMCP). It demonstrates the prescription information of Chinese patent medicines (CPMs) and ancient Chinese medicine prescriptions (CMPs). CPMCP reports their comprehensive and standardized information such as the components, indications and contraindications. It is worth mentioning that we organized relevant experts and spent lots of time manually mapping the functions of compound prescriptions in ancient Chinese to the standardized TCM symptom vocabularies, obtaining a total of 71 414 associations between compound prescriptions and TCM symptoms. In this way, CPMCP established the associations between TCM and modern medicine (MM) according to the associations between TCM symptoms and MM symptoms. In addition, to further exhibit the compatibility mechanism of compound prescriptions, CPMCP summarizes a set of common drug combination principles by analyzing the existing prescriptions. We believe that CPMCP can promote the modernization of TCM and make greater contributions to MM. 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It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. In our study, we successfully compressed the VCF files from the 1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 million variants, from an uncompressed VCF file of 803.70GB to approximately 1GB.", "homepage": "https://github.com/luo-xiaolong/GSC", "biotoolsID": "gsc_genotype_sparse_compression", "biotoolsCURIE": "biotools:gsc_genotype_sparse_compression", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "admin", "additionDate": "2024-03-05T01:49:53.830800Z", "lastUpdate": "2026-05-05T08:11:45.079709Z", "editPermission": { "type": "group", "authors": [ "MarcoFerrari11" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Hifiasm", "description": "Hifiasm: a haplotype-resolved assembler for accurate Hifi reads", "homepage": "https://github.com/chhylp123/hifiasm", "biotoolsID": "hifiasm", "biotoolsCURIE": "biotools:hifiasm", "version": [ "0.16.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "C", "C++" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://hifiasm.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/s41592-020-01056-5", "pmid": "33526886", "pmcid": "PMC7961889", "type": [], "version": null, "note": null, "metadata": { "title": "Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm", "abstract": "Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. 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