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1
Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers. J Phys Chem Lett 2019;10:7333-7339. [PMID: 31714784 DOI: 10.1021/acs.jpclett.9b02861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
2
A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics. J Chem Theory Comput 2018;14:6093-6101. [PMID: 30208708 DOI: 10.1021/acs.jctc.8b00687] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
3
Small compounds modulating bi‐directional allostery in protein kinases: a new grip with an old trick. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.797.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
4
Assessment of the model refinement category in CASP12. Proteins 2017;86 Suppl 1:152-167. [PMID: 29071750 DOI: 10.1002/prot.25409] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/03/2017] [Accepted: 10/24/2017] [Indexed: 01/07/2023]
5
An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. J Chem Inf Model 2017;57:1210-1217. [PMID: 28453271 DOI: 10.1021/acs.jcim.6b00772] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
6
Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations. Chem Sci 2017;8:4019-4026. [PMID: 30155211 PMCID: PMC6094175 DOI: 10.1039/c6sc04647a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/24/2017] [Indexed: 12/27/2022]  Open
7
Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations. eLife 2017;6. [PMID: 28445123 PMCID: PMC5406204 DOI: 10.7554/elife.22175] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/06/2017] [Indexed: 01/03/2023]  Open
8
Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017;7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023]  Open
9
Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations. J Am Chem Soc 2016;138:14257-14263. [PMID: 27726386 DOI: 10.1021/jacs.6b05425] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
10
Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol 2016;23:1193-1205. [PMID: 27693059 DOI: 10.1016/j.chembiol.2016.06.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/06/2016] [Accepted: 06/30/2016] [Indexed: 01/10/2023]
11
Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome. Sci Rep 2016;6:30293. [PMID: 27456546 PMCID: PMC4960638 DOI: 10.1038/srep30293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/01/2016] [Indexed: 10/25/2022]  Open
12
Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling. Cancer Cell 2016;30:176-178. [PMID: 27479031 DOI: 10.1016/j.ccell.2016.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
13
A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors. Angew Chem Int Ed Engl 2016;55:8008-12. [DOI: 10.1002/anie.201602729] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/06/2016] [Indexed: 01/26/2023]
14
A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
15
11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. J Cheminform 2016;8:18. [PMID: 29270804 PMCID: PMC4896257 DOI: 10.1186/s13321-016-0119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
16
Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase. Sci Rep 2016;6:24439. [PMID: 27087366 PMCID: PMC4834493 DOI: 10.1038/srep24439] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/29/2016] [Indexed: 01/06/2023]  Open
17
An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase. Sci Rep 2016;6:24235. [PMID: 27063862 PMCID: PMC4827121 DOI: 10.1038/srep24235] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/22/2016] [Indexed: 11/09/2022]  Open
18
The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016;116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
19
Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics. PLoS Comput Biol 2015;11:e1004578. [PMID: 26606374 PMCID: PMC4659586 DOI: 10.1371/journal.pcbi.1004578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/01/2015] [Indexed: 11/18/2022]  Open
20
New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations. J Chem Theory Comput 2015;11:1354-9. [PMID: 26574347 DOI: 10.1021/ct5010164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
21
Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms. Acc Chem Res 2015;48:277-85. [PMID: 25496113 DOI: 10.1021/ar500356n] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
22
Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling. Cancer Cell 2013;23:489-501. [PMID: 23597563 DOI: 10.1016/j.ccr.2013.02.018] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/12/2012] [Accepted: 02/19/2013] [Indexed: 01/12/2023]
23
Intrarticular treatment of osteoartropaty knee with polynucleotides: a pilot study with medium-term follow-up. J BIOL REG HOMEOS AG 2013;27:543-549. [PMID: 23830403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
24
Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables. PHYSICAL REVIEW LETTERS 2013;110:108106. [PMID: 23521305 DOI: 10.1103/physrevlett.110.108106] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Indexed: 06/01/2023]
25
The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor. Angew Chem Int Ed Engl 2013;52:4582-6. [PMID: 23441033 DOI: 10.1002/anie.201209660] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/16/2013] [Indexed: 01/21/2023]
26
The Mechanism of Allosteric Coupling in Choline Kinase α1 Revealed by the Action of a Rationally Designed Inhibitor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
27
New Insights in Protein Kinase Conformational Dynamics. Curr Top Med Chem 2012;12:1889-95. [DOI: 10.2174/156802612804547407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 11/22/2022]
28
Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors. J Chem Theory Comput 2012;8:1165-70. [DOI: 10.1021/ct3001377] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
29
A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding. J Chem Theory Comput 2011;7:3846-52. [PMID: 26598273 DOI: 10.1021/ct200471w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
30
Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece. J Chem Theory Comput 2011;7:2675-80. [PMID: 26605458 DOI: 10.1021/ct2002489] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Metadynamics Study of a β-Hairpin Stability in Mixed Solvents. J Am Chem Soc 2011;133:2897-903. [DOI: 10.1021/ja105030m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Treatment of lesions of the rotator cuff. J BIOL REG HOMEOS AG 2010;24:453-459. [PMID: 21122285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
33
In silico design of tubulin-targeted antimitotic peptides. Nat Chem 2009;1:642-8. [DOI: 10.1038/nchem.401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 09/08/2009] [Indexed: 11/09/2022]
34
DENPOL: A new program to determine electron densities of polypeptides using extremely localized molecular orbitals. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
35
A molecular dynamics study of an endostatin-derived peptide with antiangiogenic activity and of its mutants. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.02.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
36
Study of immunological parameters in farmer's lung. CLINICAL ALLERGY 1983;13:443-9. [PMID: 6605219 DOI: 10.1111/j.1365-2222.1983.tb02620.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
37
Polyvinyl chloride pneumoconiosis: epidemiological study of exposed workers. JOURNAL OF OCCUPATIONAL MEDICINE. : OFFICIAL PUBLICATION OF THE INDUSTRIAL MEDICAL ASSOCIATION 1979;21:540-2. [PMID: 469619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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