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Publication Listing for the MeSH term molecular dynamics. Found 15 abstracts

Hall KW, Sirk TW, Percec S, Klein ML, Shinoda W. Monodisperse Polymer Melts Crystallize via Structurally Polydisperse Nanoscale Clusters: Insights from Polyethylene. Polymers (Basel). 2020 Feb 14;12(2).   PMCID: PMC7077701
Nilov D, Maluchenko N, Kurgina T, Pushkarev S, Lys A, Kutuzov M, Gerasimova N, Feofanov A, Svedas V, Lavrik O, Studitsky VM. Molecular Mechanisms of PARP-1 Inhibitor 7-Methylguanine. International journal of molecular sciences. 2020 Mar 20;21(6).   PMCID: PMC7139824
Alkhalifa S, Jennings M, Granata D, Klein M, Wuest WM, Minbiole K, Carnevale V. Analysis of the Destabilization of Bacterial Membranes by Quaternary Ammonium Compounds: A Combined Experimental and Computational Study. Chembiochem. 2019 Dec 20;.
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
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
Ge Y, Borne E, Stewart S, Hansen MR, Arturo EC, Jaffe EK, Voelz VA. Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding. The Journal of biological chemistry. 2018 Dec 21;293(51):19532-43.   PMCID: PMC6314134
Chen M, Ko HY, Remsing RC, Calegari Andrade MF, Santra B, Sun Z, Selloni A, Car R, Klein ML, Perdew JP, Wu X. Ab initio theory and modeling of water. Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):10846-51.   PMCID: PMC5642722
Dickson A, Bailey CT, Karanicolas J. Optimal allosteric stabilization sites using contact stabilization analysis. Journal of computational chemistry. 2017 Jun 05;38(15):1138-46.   PMCID: PMC5403592
Razavi AM, Delemotte L, Berlin JR, Carnevale V, Voelz VA. Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity. The Journal of biological chemistry. 2017 Jul 28;292(30):12412-23.   PMCID: PMC5535017
Pantelopulos GA, Mukherjee S, Voelz VA. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins. 2015 Sep;83(9):1665-76.
Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. Journal of computational chemistry. 2015 Sep 05;36(23):1772-85.   PMCID: PMC4512903
Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE. Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. mAbs. 2013 Mar;5(2):306-22.
Yasaka Y, Klein ML, Nakahara M, Matubayasi N. Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T-1 measurements. J Chem Phys. 2012 Feb;136(7):12.
Kuduva SS, Sarma J, Katz AK, Carrell HL, Desiraju GR. Melting-points of the meta- and para-isomers of anisylpinacolone. Journal of Physical Organic Chemistry. 2000 Nov;13(11):719-28.
Laub PB, Khorasanizadeh S, Roder H. Localized Solution Structure Refinement of an F45w Variant of Ubiquitin Using Stochastic Boundary Molecular-Dynamics and Nmr Distance Restraints. Protein Science. 1995 May;4(5):973-82.
The above publications are sorted by year, faculty last name, and first author. Click on any highlighted author listed to find all publications attributed to that individual. Click on the publication title to see the abstract. First authors who are faculty are highlighted like this. Last authors who are faculty are highlighted like this. Other authors who are faculty are highlighted like this.

MeSH cloud from publications including the MeSH term molecular dynamics

molecular dynamics simulations protein conformational changes simulation allosteric material regulation elastic network models energy landscape water fluorescence anisotropy signal transduction Allostery protein function allosteric drugs allosteric switches enthalpy protein stabilization proton magnetic resonance allosteric regulation sodium transport FLUORESCENCE inhibitor intermolecular interactions stability Fourier transforms Membrane Transporter CANONICAL STRUCTURES CATION FORCE-FIELD efficiency analysis binding pathways nucleosome site- monoclonal antibodies quaternary ammonium compound directed mutagenesis 7-methylguanine MDM2 lid region ab initio theory COMPLEMENT ACTIVATION poly(ADP-ribose) polymerase 1 3-dimensional structures binding energy distribution analysis method MODEL-FREE APPROACH anisylpinacolone dispersity packing energy genetics structure Na+ ATOM FORCE-FIELD Selectivity potassium transport ligand-binding protein allostery chemical rescue MACROMOLECULES conformational change polyethylene nuclear-magnetic-resonance receptor flexibility protein structures DIELECTRIC RESPONSE Allosteric Regulation Thermodynamics Atomic Physics-Molecular & Chemical conotoxin gvia Research & Experimental Medicine Allosteric Site relaxation matrix omega- IMMUNOGLOBULIN-G Drug Design spectroscopy DEPENDENCE nucleation membrane transport chemical shift prediction docking coarse-grained model asynchronous replica exchange simulated annealing Proteins CHIMERIC HUMAN protein re-activation stem ligand binding kinetics host-guest system organic compounds trapping SOLVATION DYNAMICS Molecular Dynamics Simulation melting-point Free energy perturbation K+-ATPase protein Markov State Models metabolism protein binding kinetics solution dynamics GAUSSIAN NETWORK MODEL crystallization PROTEIN DYNAMICS liquid structure Genetic Transcription 1-BUTYL-3-METHYLIMIDAZOLIUM HEXAFLUOROPHOSPHATE distributed computing network hydrogen bonding Gene Expression Regulation entropy SEGMENTAL FLEXIBILITY method spFRET microscopy Metabolic Networks and Pathways lipids lysozyme geometry HINGE REGION chemistry Biosensing Techniques nuclear overhauser effect Protonation therapeutic antibodies crystal structure Anion binding site antibacterial diffusion density functional theory PK(A) VALUES MAGNETIC-RESONANCE RELAXATION relaxation matrix analysis Signal Transduction
Last updated on Saturday, July 04, 2020