ArticleNucleic acids research2017
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 42 citations in OpenAlex.
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- CAPIM: Catalytic activity and site prediction and analysis tool in multimer proteins.Protein science : a publication of the Protein Society · 2025Article
- In Silico Drug Repurposing Endorse Amprenavir, Darunavir and Saquinavir to Target Enzymes of Multidrug Resistant UropathogenicIndian journal of microbiology · 2024Article
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- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- COLLAPSE: A representation learning framework for identification and characterization of protein structural sites.Protein science : a publication of the Protein Society · 2023Article
- Specifics of Metabolite-Protein Interactions and Their Computational Analysis and Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Review
- MSALigMap-A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function.Life (Basel, Switzerland) · 2022Article
- Inhibitory Effects of Bacterial Silk-like Biopolymer on Herpes Simplex Virus Type 1, Adenovirus Type 7 and Hepatitis C Virus Infection.Journal of functional biomaterials · 2022Article
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- Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins.Journal of biological research (Thessalonike, Greece) · 2021Article
- Demystifying Chronic Kidney Disease of Unknown Etiology (CKDu): Computational Interaction Analysis of Pesticides and Metabolites with Vital Renal Enzymes.Biomolecules · 2021Article
- IHEC_RAAC: a online platform for identifying human enzyme classes via reduced amino acid cluster strategy.Amino acids · 2021Article
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- High precision protein functional site detection using 3D convolutional neural networks.Bioinformatics (Oxford, England) · 2019Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/.
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