Literature DB >> 17996742

Flexible ligand-flexible protein docking in protein kinase systems.

Chung F Wong1.   

Abstract

Quite a few reviews on molecular docking have already appeared. This mini-review focuses on methods that incorporate protein flexibility in docking rather than those that treat protein targets as rigid molecules. This is still a challenging problem but there are encouraging recent advances. These methods will be reviewed particularly in light of their applications to protein kinases and phosphatases. In addition to obtaining correct docking pose, recent developments on exploring docking pathways are also highlighted.

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Year:  2007        PMID: 17996742     DOI: 10.1016/j.bbapap.2007.10.005

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  17 in total

1.  Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability.

Authors:  Anshuman Dixit; Ali Torkamani; Nicholas J Schork; Gennady Verkhivker
Journal:  Biophys J       Date:  2009-02       Impact factor: 4.033

2.  Molecular motions in drug design: the coming age of the metadynamics method.

Authors:  Xevi Biarnés; Salvatore Bongarzone; Attilio Vittorio Vargiu; Paolo Carloni; Paolo Ruggerone
Journal:  J Comput Aided Mol Des       Date:  2011-02-17       Impact factor: 3.686

3.  Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases.

Authors:  Chung F Wong
Journal:  Protein Sci       Date:  2015-06-22       Impact factor: 6.725

4.  Insights from free-energy calculations: protein conformational equilibrium, driving forces, and ligand-binding modes.

Authors:  Yu-Ming M Huang; Wei Chen; Michael J Potter; Chia-En A Chang
Journal:  Biophys J       Date:  2012-07-17       Impact factor: 4.033

5.  Illuminating the molecular mechanisms of tyrosine kinase inhibitor resistance for the FGFR1 gatekeeper mutation: the Achilles' heel of targeted therapy.

Authors:  Christal D Sohl; Molly R Ryan; BeiBei Luo; Kathleen M Frey; Karen S Anderson
Journal:  ACS Chem Biol       Date:  2015-02-24       Impact factor: 5.100

6.  Predicting the accuracy of protein-ligand docking on homology models.

Authors:  Annalisa Bordogna; Alessandro Pandini; Laura Bonati
Journal:  J Comput Chem       Date:  2011-01-15       Impact factor: 3.376

7.  Automated site preparation in physics-based rescoring of receptor ligand complexes.

Authors:  Chaya S Rapp; Cheryl Schonbrun; Matthew P Jacobson; Chakrapani Kalyanaraman; Niu Huang
Journal:  Proteins       Date:  2009-10

8.  A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3β, and CDK2/Cyclin A protein kinases.

Authors:  Yingting Liu; Neeraj J Agrawal; Ravi Radhakrishnan
Journal:  J Mol Model       Date:  2012-08-29       Impact factor: 1.810

9.  Computational evaluation of protein-small molecule binding.

Authors:  Olgun Guvench; Alexander D MacKerell
Journal:  Curr Opin Struct Biol       Date:  2009-01-21       Impact factor: 6.809

Review 10.  Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.

Authors:  Zhiye Tang; Christopher C Roberts; Chia-En A Chang
Journal:  Front Biosci (Landmark Ed)       Date:  2017-01-01
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