Literature DB >> 30739726

Will the Real Cryptic Pocket Please Stand Out?

Rommie E Amaro1.   

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Year:  2019        PMID: 30739726      PMCID: PMC6400825          DOI: 10.1016/j.bpj.2019.01.018

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


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  14 in total

1.  Discovery of a novel binding trench in HIV integrase.

Authors:  Julie R Schames; Richard H Henchman; Jay S Siegel; Christoph A Sotriffer; Haihong Ni; J Andrew McCammon
Journal:  J Med Chem       Date:  2004-04-08       Impact factor: 7.446

2.  Clustering by passing messages between data points.

Authors:  Brendan J Frey; Delbert Dueck
Journal:  Science       Date:  2007-01-11       Impact factor: 47.728

3.  Markov models of molecular kinetics: generation and validation.

Authors:  Jan-Hendrik Prinz; Hao Wu; Marco Sarich; Bettina Keller; Martin Senne; Martin Held; John D Chodera; Christof Schütte; Frank Noé
Journal:  J Chem Phys       Date:  2011-05-07       Impact factor: 3.488

4.  Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.

Authors:  Justin R Porter; Katelyn E Moeder; Carrie A Sibbald; Maxwell I Zimmerman; Kathryn M Hart; Michael J Greenberg; Gregory R Bowman
Journal:  Biophys J       Date:  2019-01-25       Impact factor: 4.033

Review 5.  Markov State Models: From an Art to a Science.

Authors:  Brooke E Husic; Vijay S Pande
Journal:  J Am Chem Soc       Date:  2018-02-02       Impact factor: 15.419

6.  Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations.

Authors:  Vladimiras Oleinikovas; Giorgio Saladino; Benjamin P Cossins; Francesco L Gervasio
Journal:  J Am Chem Soc       Date:  2016-10-20       Impact factor: 15.419

Review 7.  Ensemble Docking in Drug Discovery.

Authors:  Rommie E Amaro; Jerome Baudry; John Chodera; Özlem Demir; J Andrew McCammon; Yinglong Miao; Jeremy C Smith
Journal:  Biophys J       Date:  2018-03-30       Impact factor: 4.033

8.  Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53.

Authors:  Christopher D Wassman; Roberta Baronio; Özlem Demir; Brad D Wallentine; Chiung-Kuang Chen; Linda V Hall; Faezeh Salehi; Da-Wei Lin; Benjamin P Chung; G Wesley Hatfield; A Richard Chamberlin; Hartmut Luecke; Richard H Lathrop; Peter Kaiser; Rommie E Amaro
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

Review 9.  Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

Authors:  Jeffrey R Wagner; Christopher T Lee; Jacob D Durrant; Robert D Malmstrom; Victoria A Feher; Rommie E Amaro
Journal:  Chem Rev       Date:  2016-04-13       Impact factor: 60.622

10.  Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis.

Authors:  Giuseppina La Sala; Sergio Decherchi; Marco De Vivo; Walter Rocchia
Journal:  ACS Cent Sci       Date:  2017-08-10       Impact factor: 14.553

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  1 in total

1.  Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.

Authors:  Richard D Smith; Heather A Carlson
Journal:  J Chem Inf Model       Date:  2021-02-18       Impact factor: 4.956

  1 in total

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