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Publication Listing for the MeSH term Molecular Models. Found 77 abstracts

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Stromyer ML, Southerland MR, Satyal U, Sikder RK, Weader DJ, Baughman JA, Youngs WJ, Abbosh PH. Synthesis, characterization, and biological activity of a triphenylphosphonium-containing imidazolium salt against select bladder cancer cell lines. European journal of medicinal chemistry. 2020 Jan;185:111832.
Wan H, Ge Y, Razavi A, Voelz VA. Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models. J Chem Theory Comput. 2020 Feb 11;16(2):1333-48.
Haldane A, Levy RM. Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. Physical review E. 2019 Mar;99(3-1):032405.   PMCID: PMC6508952
Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu-Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. eLife. 2019 May 23;8.   PMCID: PMC6581505
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
Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nature protocols. 2018 Nov;13(11):2535-56.   PMCID: PMC6322412
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. Science translational medicine. 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 (London, England : 1993). 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.
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 Thermodynamics Proteins Protein Conformation HIV Integrase genetics Computer Simulation Ligands Allosteric Regulation HIV Integrase Inhibitors Protein Folding Structure-Activity Relationship drug effects pathology Secondary Protein Structure Molecular Structure Male methods Software Tumor Cell Line statistics & numerical data pharmacology Mice Algorithms integrase Quantum Theory Statistical Models Genetic Models Chemical Models Protein Databases Protein Multimerization drug therapy Protein Binding Protein Structural Homology Computational Biology Protein Domains HEK293 Cells HIV-1 Amino Acid Sequence Reactive Oxygen Species HIV-1 integrase PL-fluorophenyl PL-FPh HIV Infections Female virology Proto-Oncogene Proteins c-met Down-Regulation Antineoplastic Agents cancer Apoptosis force field medicinal chemistry Piperlongumine PL kinase Oxidation-Reduction Triphenylphosphonium salt HeLa Cells Mitogen-Activated Protein Kinase 14 Internet Mutation Factor Xa DNA Footprinting Signal transducer and activator of transcription STAT Molecular Docking Simulation Prions Potts model Ros protein-ligand binding Vascular endothelial growth factor receptor VEGFR Solutions Middle Aged allosteric inhibitor Peptoids piperlongumine Thiophenes conformational preference infectious disease Overnutrition homology modeling Organophosphorus Compounds DNA-Directed DNA Polymerase Ribonucleic acid RNA Renal cell carcinoma RCC Complementarity Determining Regions fragment screening Solvents Casp Bedam Monte Carlo Method microbiology Insulin Resistance Amino Acid Motifs Hydroxyl Radical Polyacrylamide Gel Electrophoresis Carboxylic Acids Catalytic Domain Mitogen-activated protein kinase MAPK Binding Sites X-Ray Crystallography Experimental Neoplasms drug screening Kinetics Oxidative Stress Hepatocyte growth factor HGF Water Isomerism Molecular Evolution Protein Aggregates Drosophila melanogaster Imidazoles Gist Stereoisomerism protein-protein docking Protein Carbonylation Health free energy Nuclear factor kappaB NF-kB Markov Chains Urinary Bladder Neoplasms HIV Protease Double-Stranded DNA Breaks Protein Footprinting Drug Design virus DNA End-Joining Repair Extracellular signal-regulated kinase Erk Protein Kinase Inhibitors human immunodeficiency virus (HIV) immunology chemical synthesis inhibitor specificity allosteric HIV-1 integrase inhibitor DNA Antigen-Antibody Complex Drug Discovery declared Archaea Myoglobin Tyrosine kinase inhibitors TKIs Bacteria Dioxolanes Adenine enzymology Bayes Theorem co-evolution physiology Nucleosomes Drug Dose-Response Relationship
Last updated on Saturday, August 15, 2020