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Publication Listing for the MeSH term Molecular Models. Found 72 abstracts

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Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. PLoS computational biology. 2018 Apr 27;14(4):e1006112.   PMCID: PMC5942852
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
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.
Malhotra S, Karanicolas J. When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?. Journal of medicinal chemistry. 2017 Jan 12;60(1):128-45.   PMCID: PMC5525026
An Y, Doney AC, Andrade RB, Wheeler SE. Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals. Journal of chemical information and modeling. 2016 May 23;56(5):906-14.
Deng N, Hoyte A, Mansour YE, Mohamed MS, Fuchs JR, Engelman AN, Kvaratskhelia M, Levy R. Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies. Protein science : a publication of the Protein Society. 2016 Nov;25(11):1911-7.   PMCID: PMC5079246
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
Modi V, Xu Q, Adhikari S, Dunbrack RL. Assessment of template-based modeling of protein structure in CASP11. Proteins. 2016 Sep;84 Suppl 1:200-20.   PMCID: PMC5030193
Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. The Journal of biological chemistry. 2016 Nov 04;291(45):23569-77.   PMCID: PMC5095411
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
Boden G, Homko C, Barrero CA, Stein TP, Chen X, Cheung P, Fecchio C, Koller S, Merali S. Excessive caloric intake acutely causes oxidative stress, GLUT4 carbonylation, and insulin resistance in healthy men. Sci Transl Med. 2015 Sep 09;7(304):304re7.   PMCID: PMC5600191
Golovine K, Makhov P, Naito S, Raiyani H, Tomaszewski J, Mehrazin R, Tulin A, Kutikov A, Uzzo RG, Kolenko VM. Piperlongumine and its analogs down-regulate expression of c-Met in renal cell carcinoma. Cancer Biology & Therapy. 2015 May;16(5):743-9.   PMCID: 4623021
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. 2015 Sep;23(9):1735-42.   PMCID: 4640677
Kent T, Chandramouly G, McDevitt SM, Ozdemir AY, Pomerantz RT. Mechanism of microhomology-mediated end-joining promoted by human DNA polymerase theta. Nature structural & molecular biology. 2015 Mar;22(3):230-7.   PMCID: PMC4351179
Mukherjee S, Zhou G, Michel C, Voelz VA. Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential. J Phys Chem B. 2015 Dec 17;119(50):15407-17.
Vijayan RS, He P, Modi V, Duong-Ly KC, Ma HC, Peterson JR, Dunbrack RL, Levy RM. Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors. Journal of medicinal chemistry. 2015 Jan;58(1):466-79.   PMCID: 4326797
Thomas CJ, Kotova E, Andrake M, Adolf-Bryfogle J, Glaser R, Regnard C, Tulin AV. Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. Molecular cell. 2014 Mar 06;53(5):831-42.   PMCID: PMC3951681
Wagner J, Kline CL, Pottorf RS, Nallaganchu BR, Olson GL, Dicker DT, Allen JE, El-Deiry WS. The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity. Oncotarget. 2014 Dec 30;5(24):12728-37.   PMCID: PMC4350349
Yang J, Zhu L, Zhang H, Hirbawi J, Fukuda K, Dwivedi P, Liu J, Byzova T, Plow EF, Wu J, Qin J. Conformational activation of talin by RIAM triggers integrin-mediated cell adhesion. Nat Commun. 2014 Dec 18;5:5880.   PMCID: 4432866
Zhang H, Chang YC, Brennan ML, Wu J. The structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism. J Mol Cell Biol. 2014 Apr;6(2):128-39.   PMCID: 4817127
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 Models

Molecular Models chemistry metabolism Protein Binding Protein Conformation genetics Thermodynamics Ligands Molecular Structure Mice Allosteric Regulation Protein Structural Homology Secondary Protein Structure Protein Databases Structure-Activity Relationship Amino Acid Sequence Protein Folding Tertiary Protein Structure X-Ray Crystallography Tumor Cell Line Molecular Conformation pharmacology HIV Integrase Software HIV-1 integrase antagonists & inhibitors Computer Simulation Computational Biology Quantum Theory Amino Acid Motifs methods Cell Adhesion Signal Transduction Reactive Oxygen Species HIV Integrase Inhibitors pathology statistics & numerical data Membrane Proteins Protein Kinase Inhibitors HIV-1 Signal Transducing Adaptor Proteins Proteins Cell Membrane drug effects Male HIV Infections Protein Kinases virology Proto-Oncogene Proteins c-met Down-Regulation Antineoplastic Agents cancer Cricetulus force field medicinal chemistry Piperlongumine PL Riam kinase Chemical Models Drosophila Oxidation-Reduction Mitogen-Activated Protein Kinase 14 Mutation Internet Factor Xa Signal transducer and activator of transcription STAT Molecular Docking Simulation Prions Potts model Real-Time Polymerase Chain Reaction Ros protein-ligand binding Reproducibility of Results Vascular endothelial growth factor receptor VEGFR Telomere-Binding Proteins Middle Aged allosteric inhibitor Peptoids Biocatalysis piperlongumine Thiophenes conformational preference Overnutrition homology modeling DNA-Directed DNA Polymerase Ribonucleic acid RNA Renal cell carcinoma RCC Complementarity Determining Regions fragment screening Solvents Casp Open Reading Frames Bedam Monte Carlo Method Insulin Resistance Protein Multimerization Poly(ADP-ribose) Polymerases Small Molecule Libraries Carboxylic Acids Catalytic Domain Mitogen-activated protein kinase MAPK Binding Sites integrase Poly Adenosine Diphosphate Ribose inside-out signaling drug screening Immunohistochemistry Kinetics Oxidative Stress Hepatocyte growth factor HGF Magnetic Resonance Imaging Rap1 Water Isomerism Platelet Glycoprotein GPIIb-IIIa Complex Molecular Evolution Protein Aggregates Drosophila melanogaster Histones ras Proteins Ra-ph Protein Transport Gist protein-protein docking Phosphorylation Protein Carbonylation Algorithms Health free energy Nuclear factor kappaB NF-kB HEK293 Cells Allosteric Site HIV Protease Talin Double-Stranded DNA Breaks Drug Design integrin signaling Protein Domains DNA End-Joining Repair Recombinant Proteins Mass Spectrometry Extracellular signal-regulated kinase Erk human immunodeficiency virus (HIV) immunology inhibitor specificity allosteric HIV-1 integrase inhibitor DNA Antigen-Antibody Complex Drug Discovery Archaea
Last updated on Tuesday, December 04, 2018