AFAL: A web service for profiling amino acids surrounding ligands in proteins

Mauricio Arenas-Salinas, Samuel Ortega-Salazar, Fernando Gonzales-Nilo, Ehmke Pohl, David S. Holmes, Raquel Quatrini

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

Abstract

With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5′-triphosphate.

Original languageEnglish
Pages (from-to)1069-1076
Number of pages8
JournalJournal of Computer-Aided Molecular Design
Volume28
Issue number11
DOIs
Publication statusPublished - Nov 2014

Keywords

  • AFAL
  • Bioinformatics
  • Drug design
  • Enzyme engineering
  • PDB
  • Protein-ligand interactions

ASJC Scopus subject areas

  • Drug Discovery
  • Computer Science Applications
  • Physical and Theoretical Chemistry

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