ArticleEuropean biophysics journal : EBJ2010
How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis.
Article in European biophysics journal : EBJ, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Extended Sampling of Macromolecular Conformations from Uniformly Distributed Points on Multidimensional Normal Mode Hyperspheres.Journal of chemical theory and computation · 2024Article
- Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.Journal of chemical theory and computation · 2019Article
- re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling.BMC structural biology · 2018Article
- How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study.Scientific reports · 2017Article
- Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds.Journal of cheminformatics · 2017Article
- DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.Journal of medicinal chemistry · 2016Article
- vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available.Journal of cheminformatics · 2016Article
- ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.Nucleic acids research · 2015Article
- Polyphony: superposition independent methods for ensemble-based drug discovery.BMC bioinformatics · 2014Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
- Receptor-ligand molecular docking.Biophysical reviews · 2014Review
- Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach.PloS one · 2014Article
- In silico mechanistic profiling to probe small molecule binding to sulfotransferases.PloS one · 2013Article
- Pocket-based drug design: exploring pocket space.The AAPS journal · 2013Review
- Protein flexibility in docking and surface mapping.Quarterly reviews of biophysics · 2012Review
- Structure-based virtual screening for drug discovery: a problem-centric review.The AAPS journal · 2012Review
- PSCDB: a database for protein structural change upon ligand binding.Nucleic acids research · 2012Article
- Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures.Journal of chemical information and modeling · 2011Article
- Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.Protein science : a publication of the Protein Society · 2011Review
- Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.BMC structural biology · 2011Article
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Authors and funding
6 authors.
Funding
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Abstract
Better treatment of protein flexibility is essential in structure-based drug design projects such as virtual screening and protein-ligand docking. Diversity in ligand-binding mechanisms and receptor conformational changes makes it difficult to treat dynamic features of the receptor during the docking simulation. Thus, the use of pregenerated multiple receptor conformations is applied today in virtual screening studies. However, generation of a small relevant set of receptor conformations remains challenging. To address this problem, we propose a new protocol for the generation of multiple receptor conformations via normal mode analysis and for the selection of several receptor conformations suitable for docking/virtual screening. We validated this protocol on cyclin-dependent kinase 2, which possesses a binding site located at the interface between two subdomains and is known to undergo significant conformational changes in the active site region upon ligand binding. We believe that the suggested rules for the choice of suitable receptor conformations can be applied to other targets when dealing with in silico screening on flexible receptors.
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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.