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Gaussian network model can be enhanced by combining solvent accessibility in proteins.

Zhang H, Jiang T, Shan G, Xu S, Song Y.

Sci Rep. 2017 Aug 8;7(1):7486. doi: 10.1038/s41598-017-07677-9.


Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling.

Zheng W, Wen H, Iacobucci GJ, Popescu GK.

Biophys J. 2017 Jun 20;112(12):2589-2601. doi: 10.1016/j.bpj.2017.04.043.


String method solution of the gating pathways for a pentameric ligand-gated ion channel.

Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4158-E4167. doi: 10.1073/pnas.1617567114. Epub 2017 May 9.


A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel.

Arcario MJ, Mayne CG, Tajkhorshid E.

J Biol Chem. 2017 Jun 9;292(23):9480-9492. doi: 10.1074/jbc.M117.780197. Epub 2017 Apr 18.


Effect of material flexibility on the thermodynamics and kinetics of hydrophobically induced evaporation of water.

Altabet YE, Haji-Akbari A, Debenedetti PG.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2548-E2555. doi: 10.1073/pnas.1620335114. Epub 2017 Mar 13.


A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip.

Gupta S, Chakraborty S, Vij R, Auerbach A.

J Gen Physiol. 2017 Jan;149(1):85-103. doi: 10.1085/jgp.201611673. Epub 2016 Dec 8.


Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes.

Zhang H, Jiang T, Shan G.

Biomed Res Int. 2016;2016:4354901. Epub 2016 Nov 2.


Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation.

Wen H, Qin F, Zheng W.

Proteins. 2016 Dec;84(12):1938-1949. doi: 10.1002/prot.25177. Epub 2016 Oct 24.


Multiensemble Markov models of molecular thermodynamics and kinetics.

Wu H, Paul F, Wehmeyer C, Noé F.

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):E3221-30. doi: 10.1073/pnas.1525092113. Epub 2016 May 25. Erratum in: Proc Natl Acad Sci U S A. 2017 Jul 24;:.


Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation.

Vaikuntanathan S, Rotskoff G, Hudson A, Geissler PL.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2224-30. doi: 10.1073/pnas.1513659113. Epub 2016 Mar 8.


The Hydrophobic Effect Contributes to the Closed State of a Simplified Ion Channel through a Conserved Hydrophobic Patch at the Pore-Helix Crossing.

Yonkunas M, Kurnikova M.

Front Pharmacol. 2015 Nov 27;6:284. doi: 10.3389/fphar.2015.00284. eCollection 2015.


Pathways and Barriers for Ion Translocation through the 5-HT3A Receptor Channel.

Di Maio D, Chandramouli B, Brancato G.

PLoS One. 2015 Oct 14;10(10):e0140258. doi: 10.1371/journal.pone.0140258. eCollection 2015.


Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): CLOSED AND OPEN STATE CHANNEL MODELS.

Corradi V, Vergani P, Tieleman DP.

J Biol Chem. 2015 Sep 18;290(38):22891-906. doi: 10.1074/jbc.M115.665125. Epub 2015 Jul 30.


A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G.

PLoS One. 2015 Jul 24;10(7):e0133011. doi: 10.1371/journal.pone.0133011. eCollection 2015.


Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter.

Song HD, Zhu F.

PLoS One. 2015 Jul 17;10(7):e0133388. doi: 10.1371/journal.pone.0133388. eCollection 2015.


Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA.

Neale C, Chakrabarti N, Pomorski P, Pai EF, Pomès R.

PLoS Comput Biol. 2015 Jul 16;11(7):e1004303. doi: 10.1371/journal.pcbi.1004303. eCollection 2015 Jul.


Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.

Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S.

Biophys J. 2015 Sep 15;109(6):1101-9. doi: 10.1016/j.bpj.2015.06.004. Epub 2015 Jul 2. Review.


Anomalous behavior of water inside the SecY translocon.

Capponi S, Heyden M, Bondar AN, Tobias DJ, White SH.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):9016-21. doi: 10.1073/pnas.1424483112. Epub 2015 Jul 2.


Pentameric Ligand-gated Ion Channels : Insights from Computation.

Salari R, Murlidaran S, Brannigan G.

Mol Simul. 2014 Apr 17;40(10-11):821-829.


A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation.

Zheng W, Qin F.

J Gen Physiol. 2015 May;145(5):443-56. doi: 10.1085/jgp.201411335.

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