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Publication Listing for the MeSH term Molecular Dynamics Simulation. Found 17 abstracts

Hall KW, Sirk TW, Percec S, Klein ML, Shinoda W. Divining the shape of nascent polymer crystal nuclei. The Journal of chemical physics. 2019 Oct 14;151(14):144901.
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). 2019 Apr 02;27(4):566-78.   PMCID: PMC6688844
Kasimova MA, Yazici AT, Yudin Y, Granata D, Klein ML, Rohacs T, Carnevale V. A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine. The Journal of general physiology. 2018 Nov 05;150(11):1554-66.   PMCID: PMC6219692
Kasimova MA, Yazici A, Yudin Y, Granata D, Klein ML, Rohacs T, Carnevale V. Ion Channel Sensing: Are Fluctuations the Crux of the Matter?. The journal of physical chemistry letters. 2018 Mar 15;9(6):1260-4.
Xia J, Flynn W, Levy RM. Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. Journal of chemical information and modeling. 2018 Jul 23;58(7):1356-71.   PMCID: PMC6287956
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. Journal of Chemical Theory and Computation. 2017 Jun 13;13(6):3031-48.   PMCID: PMC5717763
Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of computer-aided molecular design. 2017 Jan;31(1):29-44.   PMCID: PMC5477994
Zhou G, Pantelopulos GA, Mukherjee S, Voelz VA. Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models. Biophysical journal. 2017 Aug 22;113(4):785-93.   PMCID: PMC5567610
Gianti E, Delemotte L, Klein ML, Carnevale V. On the role of water density fluctuations in the inhibition of a proton channel. Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8359-e8368.   PMCID: PMC5206518
Wan H, Zhou G, Voelz VA. A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations. J Chem Theory Comput. 2016 Dec 13;12(12):5768-76.
Gianti E, Carnevale V, DeGrado WF, Klein ML, Fiorin G. Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors. J Phys Chem B. 2015 Jan 22;119(3):1173-83.   PMCID: PMC4386636
Tanaka N, Dutrow EV, Miyadera K, Delemotte L, MacDermaid CM, Reinstein SL, Crumley WR, Dixon CJ, Casal ML, Klein ML, Aguirre GD, Tanaka JC, Guziewicz KE. Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment. PLoS One. 2015 Jan;10(9):e0138943.   PMCID: 4583268
Wakefield AE, Wuest WM, Voelz VA. Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides. Journal of chemical information and modeling. 2015 Apr 27;55(4):806-13.
Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, Kovalevsky A. L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study. Structure (London, England : 1993). 2014 Sep 02;22(9):1287-300.
Tanaka N, Delemotte L, Klein ML, Komaromy AM, Tanaka JC. A cyclic nucleotide-gated channel mutation associated with canine daylight blindness provides insight into a role for the S2 segment tri-Asp motif in channel biogenesis. PLoS One. 2014 Jan;9(2):e88768.   PMCID: Pmc3931646
Bankura A, Carnevale V, Klein ML. Hydration structure of salt solutions from ab initio molecular dynamics. The Journal of chemical physics. 2013 Jan 07;138(1):014501.
Raju SG, Barber AF, LeBard DN, Klein ML, Carnevale V. Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation. PLoS computational biology. 2013 Jan;9(6):e1003090.   PMCID: Pmc3681623
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MeSH cloud from publications including the MeSH term Molecular Dynamics Simulation

Molecular Dynamics Simulation chemistry metabolism Thermodynamics genetics Mutation Protein Binding Protein Conformation Water Amino Acid Sequence Molecular Conformation Drug Design Hydrophobic and Hydrophilic Interactions Ion Channel Gating Binding Sites veterinary Proteins Hydrogen Bonding Dogs Kinetics TRPV Cation Channels Molecular Sequence Data Static Electricity Ligands Cyclic Nucleotide-Gated Cation Channels pharmacology Computer Simulation Salts Cyclic Peptides Tumor Suppressor Protein p53 drug design Bacterial Proteins allosteric switches Sequence Alignment Streptomyces molecular dynamics Proto-Oncogene Proteins c-mdm2 Retinal Cone Photoreceptor Cells Salt effects ROC Curve Sampl5 Protein Folding Debye-Huckel Hv1 Sodium Channels Retinal Degeneration alpha-Helical Protein Conformation Asparagine Agbnp2 Molecular Cloning allosteric material energy landscape Radiation Scattering Channelopathies Ion Channels Dog Diseases Hydration Site Analysis (HSA) Reactive Oxygen Species Solutions Metabolic Networks and Pathways Biocatalysis Area Under Curve Solvents Bedam protein conformational changes Amino Acid Motifs DNA Primers pathology Secondary Protein Structure X-Ray Crystallography protein function Immunohistochemistry Color Vision Defects Porosity Ammonium Compounds biosynthesis drug effects Stereoisomerism methods Inhibitory Concentration 50 Aldose-Ketose Isomerases Viral Matrix Proteins allosteric drugs Inhalation Anesthetics Allosteric Regulation Markov Chains Allosteric Site HIV Protease Permeability Peptidomimetics Protons Tryptophan Crystallization Peptides binding site discovery Molecular Structure DNA Sequence Analysis Fluorescence diagnosis Bacteria regulation General Anesthetics Genetic Models enzymology Genetic Transcription physiology Chemical Databases Arabinose Gene Expression Regulation Ions Computational Biology Allostery Biosensing Techniques Sequence Homology pore waters Movement Muramidase Signal Transduction Leucine Zippers Cadmium Magnesium Hydrogen antagonists & inhibitors confined waters HIV Integrase Mice Rotation Polyethylene Xylenes elastic network models Macromolecular Substances Influenza A virus Missense Mutation Substrate Specificity Time Factors Base Sequence signal transduction
Last updated on Wednesday, August 05, 2020