These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
183 related articles for article (PubMed ID: 33877634)
21. Conformational Fluctuations in GTP-Bound K-Ras: A Metadynamics Perspective with Harmonic Linear Discriminant Analysis. Wang X J Chem Inf Model; 2021 Oct; 61(10):5212-5222. PubMed ID: 34570515 [TBL] [Abstract][Full Text] [Related]
22. Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method. Molloy K; Shehu A BMC Struct Biol; 2013; 13 Suppl 1(Suppl 1):S8. PubMed ID: 24565158 [TBL] [Abstract][Full Text] [Related]
23. Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics. Chiu SH; Xie L J Chem Inf Model; 2016 Jun; 56(6):1164-74. PubMed ID: 27159844 [TBL] [Abstract][Full Text] [Related]
24. Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 Transporter. Song HD; Zhu F J Phys Chem B; 2017 Apr; 121(15):3376-3386. PubMed ID: 27959537 [TBL] [Abstract][Full Text] [Related]
25. Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins. Harada R; Shigeta Y J Chem Theory Comput; 2017 Mar; 13(3):1411-1423. PubMed ID: 28170260 [TBL] [Abstract][Full Text] [Related]
26. A Mode Evolution Metric to Extract Reaction Coordinates for Biomolecular Conformational Transitions. Das M; Venkatramani R J Chem Theory Comput; 2024 Oct; 20(19):8422-8436. PubMed ID: 39287954 [TBL] [Abstract][Full Text] [Related]
27. Conformational dynamics of cytochrome c: correlation to hydrogen exchange. GarcĂa AE; Hummer G Proteins; 1999 Aug; 36(2):175-91. PubMed ID: 10398365 [TBL] [Abstract][Full Text] [Related]
28. Experimental accuracy in protein structure refinement via molecular dynamics simulations. Heo L; Feig M Proc Natl Acad Sci U S A; 2018 Dec; 115(52):13276-13281. PubMed ID: 30530696 [TBL] [Abstract][Full Text] [Related]
29. Toward Convergence in Free Energy Calculations for Protein Conformational Changes: A Case Study on the Thin Gate of Mhp1 Transporter. Meshkin H; Zhu F J Chem Theory Comput; 2021 Oct; 17(10):6583-6596. PubMed ID: 34523931 [TBL] [Abstract][Full Text] [Related]
33. How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations. Harada R; Shigeta Y Phys Chem Chem Phys; 2018 Jul; 20(26):17790-17798. PubMed ID: 29922770 [TBL] [Abstract][Full Text] [Related]
34. Structural Validation by the Yasuda T; Morita R; Shigeta Y; Harada R J Chem Inf Model; 2022 Jul; 62(14):3442-3452. PubMed ID: 35786886 [TBL] [Abstract][Full Text] [Related]
36. Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables. Brotzakis ZF; Parrinello M J Chem Theory Comput; 2019 Feb; 15(2):1393-1398. PubMed ID: 30557019 [TBL] [Abstract][Full Text] [Related]
37. Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. Harada R; Shigeta Y J Comput Chem; 2017 Dec; 38(31):2671-2674. PubMed ID: 28861895 [TBL] [Abstract][Full Text] [Related]
38. An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber. Meral D; Provasi D; Filizola M J Chem Phys; 2018 Dec; 149(22):224101. PubMed ID: 30553249 [TBL] [Abstract][Full Text] [Related]
39. Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin. Harada R; Takano Y; Shigeta Y J Comput Chem; 2015 Apr; 36(10):763-72. PubMed ID: 25691321 [TBL] [Abstract][Full Text] [Related]