GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms

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/.

• Publication year

  2017

• Venue

  Nucleic Acids Res.

• Publication date

  2017-04-29

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkx337PMID 28459991PMCID 5570142
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• GASS: identifying enzyme active sites with genetic algorithms

  2015influential reference
• Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

  2015cited by this paper
• MeGASS: Multi-Objective Genetic Active Site Search

  2015cited by this paper
• MMDB and VAST+: tracking structural similarities between macromolecular complexes

  2013cited by this paper
• The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

  2013cited by this paper
• Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

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• SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

  2012cited by this paper
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  2010cited by this paper
• The structure of a putative S‐formylglutathione hydrolase from Agrobacterium tumefaciens

  2009cited by this paper
• Structure‐Based Prediction of Enzymes and Their Active Sites

  2008cited by this paper
• A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

  2008cited by this paper
• Methods to characterize the structure of enzyme binding sites

  2008cited by this paper
• Protein function prediction using local 3D templates.

  2005cited by this paper
• Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures

  2003cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Handbook of evolutionary computation

  1997cited by this paper
• A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex.

  1997cited by this paper
• Handbook of Evolutionary Computation

  1997cited by this paper
• The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease.

  1993cited by this paper
• Genetic Algorithms in Search Optimization and Machine Learning

  1988cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowninfluential reference

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