Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites
نویسندگان
چکیده
منابع مشابه
Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites.
The use of predicted binding sites (binding sites calculated from the protein structure alone) is evaluated here as a tool to focus the docking of small molecule ligands into protein structures, simulating cases where the real binding sites are unknown. The resulting approach consists of a few independent docking runs carried out on small boxes, centered on the predicted binding sites, as oppos...
متن کاملBSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures.
We developed BSP-SLIM, a new method for ligand-protein blind docking using low-resolution protein structures. For a given sequence, protein structures are first predicted by I-TASSER; putative ligand binding sites are transferred from holo-template structures which are analogous to the I-TASSER models; ligand-protein docking conformations are then constructed by shape and chemical match of liga...
متن کاملPredicting the accuracy of protein-ligand docking on homology models
Ligand-protein docking is increasingly used in Drug Discovery. The initial limitations imposed by a reduced availability of target protein structures have been overcome by the use of theoretical models, especially those derived by homology modeling techniques. While this greatly extended the use of docking simulations, it also introduced the need for general and robust criteria to estimate the ...
متن کاملImproving homology models for protein-ligand binding sites.
In order to improve the prediction of protein-ligand binding sites through homology modeling, we incorporate knowledge of the binding residues into the modeling framework. Residues are identified as binding or nonbinding based on their true labels as well as labels predicted from structure and sequence. The sequence predictions were made using a support vector machine framework which employs a ...
متن کاملBinding-sites Prediction Assisting Protein-protein Docking.
Most biological actions of proteins, including their ability to interact with one another, involve some specific parts of their three-dimensional structure, called binding sites. These have evolved for their ability to bind other molecules effectively and are often conserved in different proteins. Identifying protein-protein binding sites in a protein that is known to interact with other protei...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics
سال: 2009
ISSN: 0887-3585,1097-0134
DOI: 10.1002/prot.22154