Protein-small molecule docking with receptor flexibility in iMOLSDOCK.

Abstract read

In one paragraph

Article in Journal of computer-aided molecular design, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

2 authors.

D Sam PaulCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, India.ORCID 0000-0002-8272-9561

N GauthamCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, India. n_gautham@hotmail.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We have earlier reported the iMOLSDOCK technique to perform 'induced-fit' peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein-ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/ .

Indexed as

Molecular Docking SimulationAlgorithmsDatabases, ProteinLigandsPeptidesProtein BindingProtein ConformationProteinsSoftwareThermodynamicsLigandsPeptidesProteinsiMOLSDOCKInduced-fit dockingMolecular dockingMutually orthogonal Latin squaresProtein–ligand dockingSide-chain flexibility

Identifiers

PMID30128925

DOI10.1007/s10822-018-0152-8

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.