Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 28, Issue 11, Pages 1069-1076Publisher
SPRINGER
DOI: 10.1007/s10822-014-9783-6
Keywords
AFAL; Protein-ligand interactions; PDB; Drug design; Enzyme engineering; Bioinformatics
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Funding
- FONDECYT Grants (Fondo Nacional de Desarrollo Cientifico y Tecnologico) [1140048, 1130683]
- CONICYT Grant (Comision Nacional de Investigacion Cientifica y Tecnologica) [Basal CCTE PFB16]
- Santander Mobility Grant
- Durham University
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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.
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