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Publication Listing for the MeSH term Thermodynamics. Found 40 abstracts

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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
Cui D, Zhang BW, Matubayasi N, Levy RM. The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force. J Chem Theory Comput. 2018 Feb 13;14(2):512-26.   PMCID: PMC5897112
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.
Mizukami T, Xu M, Fazlieva R, Bychkova VE, Roder H. Complex Folding Landscape of Apomyoglobin at Acidic pH Revealed by Ultrafast Kinetic Analysis of Core Mutants. J Phys Chem B. 2018 Aug 31;122(49):11228-39.   PMCID: PMC6395567
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
Levy RM, Cui D, Zhang BW, Matubayasi N. Relationship between Solvation Thermodynamics from IST and DFT Perspectives. J Phys Chem B. 2017 Apr 20;121(15):3825-41.   PMCID: PMC5869707
Levy RM, Haldane A, Flynn WF. Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. Current opinion in structural biology. 2017 Apr;43:55-62.
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
Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nature protocols. 2017 Feb;12(2):401-16.   PMCID: PMC5739521
Deng N, Flynn WF, Xia J, Vijayan RS, Zhang B, He P, Mentes A, Gallicchio E, Levy RM. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. Journal of computer-aided molecular design. 2016 Sep;30(9):743-51.
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
Haldane A, Flynn WF, He P, Vijayan RS, Levy RM. Structural propensities of kinase family proteins from a Potts model of residue co-variation. Protein science : a publication of the Protein Society. 2016 Aug;25(8):1378-84.   PMCID: PMC4972195
Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of molecular recognition : JMR. 2016 Jan;29(1):10-21.   PMCID: PMC4715590
Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. J Phys Chem B. 2015 Jan 22;119(3):976-88.   PMCID: PMC4306491
Drazenovic J, Wang H, Roth K, Zhang J, Ahmed S, Chen Y, Bothun G, Wunder SL. Effect of lamellarity and size on calorimetric phase transitions in single component phosphatidylcholine vesicles. Biochim Biophys Acta. 2015 Feb;1848(2):532-43.
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
Honda RP, Xu M, Yamaguchi K, Roder H, Kuwata K. A Native-like Intermediate Serves as a Branching Point between the Folding and Aggregation Pathways of the Mouse Prion Protein. Structure (London, England : 1993). 2015 Sep;23(9):1735-42.   PMCID: 4640677
Paudyal S, Alfonso-Prieto M, Carnevale V, Redhu SK, Klein ML, Nicholson AW. Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB. Proteins. 2015 Mar;83(3):459-72.   PMCID: PMC4329070
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 Thermodynamics

Thermodynamics chemistry metabolism Molecular Dynamics Simulation Protein Binding Binding Sites Ligands genetics Protein Conformation Molecular Models Molecular Conformation Mutation Molecular Docking Simulation Kinetics Water Hydrophobic and Hydrophilic Interactions Drug Design Proteins HIV Protease Solvents Bedam Hydrogen Bonding ROC Curve Static Electricity Amino Acid Sequence methods antagonists & inhibitors Mice Protein Domains HIV Integrase Secondary Protein Structure Hydrogen-Ion Concentration Quantum Theory Oncogene Proteins v-abl Apoproteins drug design Molecular Sequence Data TRPV Cation Channels allosteric switches Sequence Alignment molecular dynamics post-transcriptional regulation Salt effects Sampl5 Protein Folding Debye-Huckel force field Roc Amino Acid Sequence Homology Hv1 kinase alpha-Helical Protein Conformation Signal Transduction Agbnp2 Muramidase Binding free energy Mitogen-Activated Protein Kinase 14 allosteric material Gel-to-liquid phase transition temperature Internet energy landscape Radiation Scattering Factor Xa Surface Properties Prions Potts model Ion Channels Sperm Whale Coupled phase transition Hydration Site Analysis (HSA) Reactive Oxygen Species Protein Unfolding Solutions Antigens Metabolic Networks and Pathways conformational preference Dimyristoylphosphatidylcholine Area Under Curve Complementarity Determining Regions ADP-ribose Movement protein conformational changes Amino Acid Motifs Lipid Bilayers Unilamellar vesicle Gc2015 pore waters protein function Gene Expression Regulation Phosphatidylcholines Site-Directed Mutagenesis 2-Dipalmitoylphosphatidylcholine 1 pharmacology Molecular Evolution Escherichia coli Proteins Carrier Proteins Porosity Protein Aggregates Phase Transition Protein Databases beta-Cyclodextrins Prospective Studies Ammonium Compounds Preclinical Drug Evaluation macrodomain Gist Allostery Inhibitory Concentration 50 free energy Viral Matrix Proteins allosteric drugs Allosteric Regulation HSP90 Heat-Shock Proteins Allosteric Site double-stranded RNA Protein Structural Homology Permeability Vesicle curvature Protons Protein Kinase Inhibitors Liposomes Hsp90 immunology Crystallization inhibitor specificity D3r binding site discovery Molecular Structure Ribonuclease III regulation Genetic Epistasis Vesicle lamellarity Biosensing Techniques co-evolution Genetic Transcription physiology Chemical Databases Solubility Dmpc Opls Hydrogen confined waters Myoglobin Polyethylene Xylenes Docking Immunoglobulin Variable Region elastic network models Macromolecular Substances Influenza A virus
Last updated on Thursday, April 02, 2020