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

Resultado de la investigación: Contribución a una revistaArtículorevisión exhaustiva

4 Citas (Scopus)

Resumen

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.

Idioma originalInglés
Páginas (desde-hasta)1069-1076
Número de páginas8
PublicaciónJournal of Computer-Aided Molecular Design
Volumen28
N.º11
DOI
EstadoPublicada - nov 2014

Áreas temáticas de ASJC Scopus

  • Descubrimiento de medicamentos
  • Informática aplicada
  • Química física y teórica

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