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{ "count": 28682, "next": "?page=2", "previous": null, "list": [ { "name": "ReRa", "description": "ReRa is a relevance-redundancy feature selection approach that improves the performance of an expression-based predictive model in unbalanced classification.", "homepage": "https://github.com/DEIB-GECO/ReRa", "biotoolsID": "rera", "biotoolsCURIE": "biotools:rera", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/DEIB-GECO/ReRa", "type": "Source code", "note": "Jupyter notebooks", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1016/j.jbi.2023.104457", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Supervised Relevance-Redundancy assessments for feature selection in omics-based classification scenarios", "abstract": "Background and objective: Many classification tasks in translational bioinformatics and genomics are characterized by the high dimensionality of potential features and unbalanced sample distribution among classes. This can affect classifier robustness and increase the risk of overfitting, curse of dimensionality and generalization leaks; furthermore and most importantly, this can prevent obtaining adequate patient stratification required for precision medicine in facing complex diseases, like cancer. Setting up a feature selection strategy able to extract only proper predictive features by removing irrelevant, redundant, and noisy ones is crucial to achieving valuable results on the desired task. Methods: We propose a new feature selection approach, called ReRa, based on supervised Relevance-Redundancy assessments. ReRa consists of a customized step of relevance-based filtering, to identify a reduced subset of meaningful features, followed by a supervised similarity-based procedure to minimize redundancy. This latter step innovatively uses a combination of global and class-specific similarity assessments to remove redundant features while preserving those differentiated across classes, even when these classes are strongly unbalanced. Results: We compared ReRa with several existing feature selection methods to obtain feature spaces on which performing breast cancer patient subtyping using several classifiers: we considered two use cases based on gene or transcript isoform expression. In the vast majority of the assessed scenarios, when using ReRa-selected feature spaces, the performances were significantly increased compared to simple feature filtering, LASSO regularization, or even MRmr — another Relevance-Redundancy method. The two use cases represent an insightful example of translational application, taking advantage of ReRa capabilities to investigate and enhance a clinically-relevant patient stratification task, which could be easily applied also to other cancer types and diseases. Conclusions: ReRa approach has the potential to improve the performance of machine learning models used in an unbalanced classification scenario. Compared to another Relevance-Redundancy approach like MRmr, ReRa does not require tuning the number of preserved features, ensures efficiency and scalability over huge initial dimensionalities and allows re-evaluation of all previously selected features at each iteration of the redundancy assessment, to ultimately preserve only the most relevant and class-differentiated features.", "date": "2023-08-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Cascianelli S." }, { "name": "Galzerano A." }, { "name": "Masseroli M." } ], "journal": "Journal of Biomedical Informatics" } } ], "credit": [ { "name": "ELIXIR-ITA", "email": null, "url": "https://elixir-italy.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [], "note": null }, { "name": "ELIXIR-ITA-POLIMI", "email": null, "url": "https://www.deib.polimi.it/eng/elixir-iib", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [], "note": null }, { "name": "Marco Masseroli", "email": "marco.masseroli@polimi.it", "url": null, "orcidid": "https://orcid.org/0000-0003-2574-1174", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Silvia Cascianelli", "email": "silvia.cascianelli@polimi.it", "url": null, "orcidid": "https://orcid.org/0000-0002-5628-9101", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Arianna Galzerano", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-POLIMI", "additionDate": "2023-11-25T09:36:19.946685Z", "lastUpdate": "2023-11-28T21:36:18.355939Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OSppc", "description": "A web server for online survival analysis using proteome of pan-cancers, including TCGA (The Cancer Genome Atlas) RPPAs (Reverse-Phase Protein Arrays) data and CPTAC (the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium) mass spectrometry data, and provides 5 types of survival terms for about 8,000 patients of 33 distinct malignancies.", "homepage": "http://bioinfo.henu.edu.cn/Protein/OSppc.html", "biotoolsID": "osppc", "biotoolsCURIE": "biotools:osppc", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" }, { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/J.JPROT.2022.104810", "pmid": "36587732", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "OSppc: A web server for online survival analysis using proteome of pan-cancers", "abstract": "Prognostic biomarker, as a feasible and objective indicator, is valuable in the assessment of cancer risk. With the development of high-throughput sequencing technology, the screening of prognostic biomarkers has become easy, but it is difficult to screen prognostic markers based on proteomic data. In this study we developed a tool named Online consensus Survival analysis web server based on Proteome of Pan-cancers, abbreviated as OSppc, to evaluate the prognostic values of protein biomarkers. >8000 cancer cases with proteomic data, transcriptomic data and clinical follow-up information were collected from TCGA and CPTAC. 14,038 proteins (including proteins and their phosphorylated forms) analyzed by reverse-phase protein arrays and mass spectrometry in 33 types of cancers were collected. In OSppc, three analysis modules are provided, including Survival Analysis, Differential Analysis and Correlation Analysis. Survival analysis module exhibits HR with 95% CI and KM curves with log-rank p value of protein and mRNA levels of input genes. Differential analysis module shows the box plots of protein expression levels in different tissues. Correlation analysis module provides scatter plot with pearson's and spearman's correlation coefficient of the protein and its corresponding mRNA. OSppc can be accessed at http://bioinfo.henu.edu.cn/Protein/OSppc.html. Significance: OSppc can analyze the association between protein, mRNA and prognosis, the correlation between proteome data and gene expression profiles, the differential expression of proteome data between subgroups such as normal and cancer as well. OSppc is registration-free and very valuable to evaluate the prognostic potency of protein of interests. OSppc is very valuable for researchers and clinicians to screen, develop and validate potential protein prognostic biomarkers in pan-cancers, and offers the opportunities to investigate the clinical important functional genes and therapeutic targets of cancers.", "date": "2023-02-20T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Zhang L." }, { "name": "Wang Q." }, { "name": "Han Y." }, { "name": "Huang Y." }, { "name": "Chen T." }, { "name": "Guo X." } ], "journal": "Journal of Proteomics" } } ], "credit": [ { "name": "Lu Zhang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Qiang Wang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiangqian Guo", "email": "xqguo@henu.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-11-28T18:51:12.437476Z", "lastUpdate": "2023-11-28T18:51:12.440050Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "vERnet-B", "description": "Artificial intelligence-based recognition for variant pathogenicity of BRCA1 using AlphaFold2-predicted structures.", "homepage": "http://ai-lab.bjrz.org.cn/vERnet", "biotoolsID": "vernet-b", "biotoolsCURIE": "biotools:vernet-b", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_3461", "term": "Virulence prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.7150/THNO.79362", "pmid": "36593954", "pmcid": "PMC9800725", "type": [], "version": null, "note": null, "metadata": { "title": "Artificial intelligence-based recognition for variant pathogenicity of BRCA1 using AlphaFold2-predicted structures", "abstract": "With the surge of the high-throughput sequencing technologies, many genetic variants have been identified in the past decade. The vast majority of these variants are defined as variants of uncertain significance (VUS), as their significance to the function or health of an organism is not known. It is urgently needed to develop intelligent models for the clinical interpretation of VUS. State-of-the-art artificial intelligence (AI)-based variant effect predictors only learn features from primary amino acid sequences, leaving out information about the most important three-dimensional structure that is more related to its function. Methods: We proposed a deep convolutional neural network model named variant effect recognition network for BRCA1 (vERnet-B) to recognize the clinical pathogenicity of missense single-nucleotide variants in the BRCT domain of BRCA1. vERnet-B learned features associated with the pathogenicity from the tertiary protein structures of variants predicted by AlphaFold2. Results: After performing a series of validation and analyses on vERnet-B, we discovered that it exhibited significant advances over previous works. Recognizing the phenotypic consequences of VUS is one of the most daunting challenges in genetic informatics; however, we achieved 85% accuracy in recognizing disease BRCA1 variants with an ideal balance of false-positive and true-positive detection rates. vERnet-B correctly recognized the pathogenicity of variant A1708E, which was poorly predicted by AlphaFold2 as previously described. The vERnet-B web server is freely available from URL: http://ai-lab.bjrz.org.cn/vERnet. Conclusions: We applied protein tertiary structures to successfully recognize the pathogenic missense SNVs, which were difficult to be addressed by classical approaches based on sequences. Our work demonstrated that AlphaFold2-predicted structures were expected to be used for rich feature learning and revealed unique insights into the clinical interpretation of VUS in disease-related genes, using vERnet-B as a discovery tool.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Li C." }, { "name": "Zhang L." }, { "name": "Zhuo Z." }, { "name": "Su F." }, { "name": "Li H." }, { "name": "Xu S." }, { "name": "Liu Y." }, { "name": "Zhang Z." }, { "name": "Xie Y." }, { "name": "Yu X." }, { "name": "Bian L." }, { "name": "Xiao F." } ], "journal": "Theranostics" } } ], "credit": [ { "name": "Xue Yu", "email": "yuxue2652@bjhmoh.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Liheng Bian", "email": "bian@bit.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Fei Xiao", "email": "xiaofei3965@bjhmoh.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-11-28T18:35:32.516382Z", "lastUpdate": "2023-11-28T18:35:32.518932Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MAD", "description": "The Martini Database (MAD) is a web server dedicated to (a) sharing structures and topologies of molecules parameterized with the Martini coarse-grained (CG) force field; (b) converting atomistic structures into CG structures; (c) preparing complex systems (including proteins, nucleic acids, lipids etc.) for molecular dynamics (MD) simulations at the CG level.", "homepage": "https://mad.ibcp.fr", "biotoolsID": "mad_cg", "biotoolsCURIE": "biotools:mad_cg", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/operation_3893", "term": "Forcefield parameterisation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/ACS.JCIM.2C01375", "pmid": "36656159", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Facilitating CG Simulations with MAD: The MArtini Database Server", "abstract": "The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.", "date": "2023-02-13T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Hilpert C." }, { "name": "Beranger L." }, { "name": "Souza P.C.T." }, { "name": "Vainikka P.A." }, { "name": "Nieto V." }, { "name": "Marrink S.J." }, { "name": "Monticelli L." }, { "name": "Launay G." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "Cécile Hilpert", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7825-9376", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Louis Beranger", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5206-2164", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Guillaume Launay", "email": "guillaume.launay@ibcp.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-0177-8706", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-11-28T18:32:13.035878Z", "lastUpdate": "2023-11-28T18:32:13.038473Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "NucEnvDB", "description": "Database of nuclear envelope proteins and their interactions.", "homepage": "http://thalis.biol.uoa.gr/nucenv-db/", "biotoolsID": "nucenvdb", "biotoolsCURIE": "biotools:nucenvdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0820", "term": "Membrane and lipoproteins" }, { "uri": "http://edamontology.org/topic_0140", "term": "Protein targeting and localisation" }, { "uri": "http://edamontology.org/topic_3957", "term": "Protein interaction experiment" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/MEMBRANES13010062", "pmid": "36676869", "pmcid": "PMC9861991", "type": [], "version": null, "note": null, "metadata": { "title": "NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions", "abstract": "The nuclear envelope (NE) is a double-membrane system surrounding the nucleus of eukaryotic cells. A large number of proteins are localized in the NE, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus to chromatin tethering, genome organization, regulation of signaling cascades, and many others. Despite its importance, several aspects of the NE, including its protein–protein interactions, remain understudied. In this work, we present NucEnvDB, a publicly available database of NE proteins and their interactions. Each database entry contains useful annotation including a description of its position in the NE, its interactions with other proteins, and cross-references to major biological repositories. In addition, the database provides users with a number of visualization and analysis tools, including the ability to construct and visualize protein–protein interaction networks and perform functional enrichment analysis for clusters of NE proteins and their interaction partners. The capabilities of NucEnvDB and its analysis tools are showcased by two informative case studies, exploring protein–protein interactions in Hutchinson–Gilford progeria and during SARS-CoV-2 infection at the level of the nuclear envelope.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Baltoumas F.A." }, { "name": "Sofras D." }, { "name": "Apostolakou A.E." }, { "name": "Litou Z.I." }, { "name": "Iconomidou V.A." } ], "journal": "Membranes" } } ], "credit": [ { "name": "Vassiliki A. Iconomidou", "email": "veconom@biol.uoa.gr", "url": null, "orcidid": "https://orcid.org/0000-0002-9472-5146", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Fotis A Baltoumas", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Dimitrios Sofras", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-11-28T18:25:05.532630Z", "lastUpdate": "2023-11-28T18:25:05.535072Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "B-LacFamPred", "description": "An online tool for prediction and classification of β-lactamase class, subclass, and family.", "homepage": "http://proteininformatics.org/mkumar/blacfampred", "biotoolsID": "b-lacfampred", "biotoolsCURIE": "biotools:b-lacfampred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3482", "term": "Antimicrobial resistance prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0865", "term": "Sequence similarity score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Perl" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mkubiophysics/B-LacFamPred", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.3389/FMICB.2022.1039687", "pmid": "36713195", "pmcid": "PMC9878453", "type": [], "version": null, "note": null, "metadata": { "title": "β-LacFamPred: An online tool for prediction and classification of β-lactamase class, subclass, and family", "abstract": "β-Lactams are a broad class of antimicrobial agents with a high safety profile, making them the most widely used class in clinical, agricultural, and veterinary setups. The widespread use of β-lactams has induced the extensive spread of β-lactamase hydrolyzing enzymes known as β-lactamases (BLs). To neutralize the effect of β-lactamases, newer generations of β-lactams have been developed, which ultimately led to the evolution of a highly diverse family of BLs. Based on sequence homology, BLs are categorized into four classes: A–D in Ambler’s classification system. Further, each class is subdivided into families. Class B is first divided into subclasses B1–B3, and then each subclass is divided into families. The class to which a BL belongs gives a lot of insight into its hydrolytic profile. Traditional methods of determining the hydrolytic profile of BLs and their classification are time-consuming and require resources. Hence we developed a machine-learning-based in silico method, named as β-LacFamPred, for the prediction and annotation of Ambler’s class, subclass, and 96 families of BLs. During leave-one-out cross-validation, except one all β-LacFamPred model HMMs showed 100% accuracy. Benchmarking with other BL family prediction methods showed β-LacFamPred to be the most accurate. Out of 60 penicillin-binding proteins (PBPs) and 57 glyoxalase II proteins, β-LacFamPred correctly predicted 56 PBPs and none of the glyoxalase II sequences as non-BLs. Proteome-wide annotation of BLs by β-LacFamPred showed a very less number of false-positive predictions in comparison to the recently developed BL class prediction tool DeepBL. β-LacFamPred is available both as a web-server and standalone tool at http://proteininformatics.org/mkumar/blacfampred and GitHub repository https://github.com/mkubiophysics/B-LacFamPred respectively.", "date": "2023-01-12T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Pandey D." }, { "name": "Singhal N." }, { "name": "Kumar M." } ], "journal": "Frontiers in Microbiology" } } ], "credit": [ { "name": "Manish Kumar", "email": "manish@south.du.ac.in", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Deeksha Pandey", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Neelja Singhal", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-11-28T18:19:35.264323Z", "lastUpdate": "2023-11-28T18:19:35.267074Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "HDXer", "description": "HDXer is a Python package that can be used to: compute Hydrogen-Deuterium exchange (HDX) data from an atomistic ensemble of protein structures and reweight a candidate ensemble by applying a maximum-entropy biasing scheme, so that the computed HDX data conform to a target experimental set of HDX-MS data, within a defined level of error.", "homepage": "https://github.com/Lucy-Forrest-Lab/HDXer", "biotoolsID": "hdxer", "biotoolsCURIE": "biotools:hdxer", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.33011/LIVECOMS.3.1.1521", "pmid": "36644498", "pmcid": "PMC9835200", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Richard T. 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Mistsis", "email": "georgios.mitsis@mcgill.ca", "url": "https://www.mcgill.ca/bbme/georgios-mitsis", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": "Assisstant Professor in Department of Biomedical Engineering at McGill University" }, { "name": "Jean-Baptiste Poline", "email": "jean-baptiste.poline@mcgill.ca", "url": "https://www.mcgill.ca/neuro/jean-baptiste-poline-phd", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": "Associate Professor, Department of Neurology and Neurosurgery, McGill University" } ], "community": null, "owner": "mtorabi00", "additionDate": "2023-11-28T04:59:55.290848Z", "lastUpdate": "2023-11-28T05:23:46.277135Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AtomicChargeCalculator", "description": "A web application for the calculation and analysis of atomic charges in both large biomolecular complexes and small drug-like molecules.", "homepage": "https://ncbr.muni.cz/ACC", "biotoolsID": "atomicchargecalculator", "biotoolsCURIE": "biotools:atomicchargecalculator", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2085", "term": "Structure report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1917", "term": "Atomic property" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C#" ], "license": null, "collectionID": [ "LCC NCBR", "Czech Republic", "ELIXIR-CZ", "CEITEC" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [ { "url": "https://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/DownloadService", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://www.jcheminf.com/content/7/1/50/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "http://webchem.ncbr.muni.cz/Wiki/ChargeCalculator:UserManual", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s13321-015-0099-x", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "AtomicChargeCalculator: Interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules", "abstract": "Background: Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. Results: This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Conclusions: Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.", "date": "2015-10-22T00:00:00Z", "citationCount": 50, "authors": [ { "name": "Ionescu C.-M." }, { "name": "Sehnal D." }, { "name": "Falginella F.L." }, { "name": "Pant P." }, { "name": "Pravda L." }, { "name": "Bouchal T." }, { "name": "Svobodova Varekova R." }, { "name": "Geidl S." }, { "name": "Koca J." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "David Sehnal", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Crina Maria Ionescu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Stanislav Geidl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Lukáš Pravda", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Primary Contact", "email": "webchemistryhelp@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "David Sehnal", "email": "david.sehnal@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Crina Maria Ionescu", "email": "crina_i@hotmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Primary Contact", "email": "webchemistryhelp@gmail.com", "url": "https://webchem.ncbr.muni.cz", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "David Sehnal", "email": "david.sehnal@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Crina Maria Ionescu", "email": "crina_i@hotmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-CZ", "additionDate": "2015-12-01T18:10:32Z", "lastUpdate": "2023-11-27T09:19:15.101428Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SpatialPath", "description": "Web application for interactive visualization of Spatial Transcriptomics datasets.", "homepage": "http://cfb.ceitec.muni.cz/spatialpath/", "biotoolsID": "spatialpath", "biotoolsCURIE": "biotools:spatialpath", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "ELIXIR-CZ", "additionDate": "2023-11-26T10:41:58.217923Z", "lastUpdate": "2023-11-26T10:41:58.220610Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }