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Regulation of RUNX2 transcription factor-DNA interactions and cell proliferation by vitamin D3 (cholecalciferol) prohormone activity.
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- Journal of Bone & Mineral Research, 2012, v. 27, n. 4, p. 913, doi. 10.1002/jbmr.1504
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- Article
In Silico Identification of a β2 Adrenergic Receptor Allosteric Site that Selectively Augments Canonical β<sub>2</sub>AR‐Gs Signaling and Function.
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- FASEB Journal, 2022, v. 36, p. N.PAG, doi. 10.1096/fasebj.2022.36.S1.R3986
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- Article
Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft.
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- BMC Structural Biology, 2007, v. 7, p. 14, doi. 10.1186/1472-6807-7-14
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- Article
Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS).
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- Molecules, 2021, v. 26, n. 2, p. 381, doi. 10.3390/molecules26020381
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- Article
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.
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- Molecules, 2018, v. 23, n. 10, p. 2695, doi. 10.3390/molecules23102695
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- Article
Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models.
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- Human Molecular Genetics, 2014, v. 23, n. 23, p. 6212
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- Article
A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells.
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- Nature Communications, 2015, v. 6, n. 6, p. 7316, doi. 10.1038/ncomms8316
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- Article
Rationally Designed Polypharmacology: α‐Helix Mimetics as Dual Inhibitors of the Oncoproteins Mcl‐1 and HDM2.
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- ChemMedChem, 2020, v. 15, n. 18, p. 1691, doi. 10.1002/cmdc.202000278
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- Article
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.
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- Journal of Molecular Modeling, 2010, v. 16, n. 3, p. 567, doi. 10.1007/s00894-009-0572-4
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- Article
GPU‐specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.
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- Journal of Computational Chemistry, 2023, v. 44, n. 20, p. 1719, doi. 10.1002/jcc.27121
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- Article
CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.
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- Journal of Computational Chemistry, 2022, v. 43, n. 5, p. 359, doi. 10.1002/jcc.26795
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- Article
Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II.
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- PLoS Pathogens, 2013, v. 9, n. 11, p. 1, doi. 10.1371/journal.ppat.1003732
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- Article
Insights into substrate recognition and specificity for IgG by Endoglycosidase S2.
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- PLoS Computational Biology, 2021, v. 17, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009103
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- Article
Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics.
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- Biopolymers, 2001, v. 61, n. 1, p. 61, doi. 10.1002/1097-0282(2001)61:1<61::AID-BIP10047>3.0.CO;2-1
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- Article
Development and current status of the CHARMM force field for nucleic acids.
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- Biopolymers, 2000, v. 56, n. 4, p. 257, doi. 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
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- Article
Nitro-benzylideneoxymorphone, a bifunctional mu and delta opioid receptor ligand with high mu opioid receptor efficacy.
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- Frontiers in Pharmacology, 2023, p. 1, doi. 10.3389/fphar.2023.1230053
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- Article
Optimization of a Benzothiazole Indolene Scaffold Targeting Bacterial Cell Wall Assembly.
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- Drug Design, Development & Therapy, 2020, v. 14, p. 567, doi. 10.2147/DDDT.S226313
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- Article
Inactivation of lactate dehydrogenase by UV radiation in the 300 nm wavelength region.
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- Acta Ophthalmologica (1755375X), 1993, v. 71, p. 185i, doi. 10.1111/j.1755-3768.1993.tb08726.x
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- Article
Cover Feature: Simple Synthesis of a Heterocyclophane Exhibiting Anti‐c‐Met Activity by Acting as a Hatch Blocking Access to the Active Site (Chem. Eur. J. 5/2021).
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- Chemistry - A European Journal, 2021, v. 27, n. 5, p. 1479, doi. 10.1002/chem.202004973
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- Article
Simple Synthesis of a Heterocyclophane Exhibiting Anti‐c‐Met Activity by Acting as a Hatch Blocking Access to the Active Site**.
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- Chemistry - A European Journal, 2021, v. 27, n. 5, p. 1648, doi. 10.1002/chem.202001382
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- Article
Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf.
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- Biochemical Journal, 2015, v. 467, n. 3, p. 425, doi. 10.1042/BJ20131571
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- Article
Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction.
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- Glycobiology, 2016, v. 26, n. 10, p. 1041, doi. 10.1093/glycob/cww073
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- Article
Reconstruction of the (011) surface on α-quartz: A semiclassical Ab initio molecular dynamics study.
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- International Journal of Quantum Chemistry, 2009, v. 109, n. 1, p. 50, doi. 10.1002/qua.21726
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- Article
Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach.
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- PLoS Computational Biology, 2013, v. 9, n. 6, p. 1, doi. 10.1371/journal.pcbi.1003113
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- Article
Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation.
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- PLoS Computational Biology, 2009, v. 5, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000435
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- Article
Polarizable Empirical Force Field for Acyclic Polyalcohols Based on the Classical Drude Oscillator.
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- Biopolymers, 2013, v. 99, n. 10, p. 724, doi. 10.1002/bip.22286
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- Article
DNA bending induced by carbocyclic sugar analogs constrained to the north conformation.
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- Biopolymers, 2007, v. 85, n. 5/6, p. 438, doi. 10.1002/bip.20673
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Recent developments and applications of the CHARMM force fields.
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- WIREs: Computational Molecular Science, 2012, v. 2, n. 1, p. 167, doi. 10.1002/wcms.74
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- Article
Structure-activity exploration of a small-molecule Lipid II inhibitor.
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- Drug Design, Development & Therapy, 2015, v. 9, p. 2383, doi. 10.2147/DDDT.S79504
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- Article
A Small Molecule Agonist of EphA2 Receptor Tyrosine Kinase Inhibits Tumor Cell Migration In Vitro and Prostate Cancer Metastasis In Vivo.
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- PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0042120
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- Article
Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis.
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- PLoS ONE, 2009, v. 4, n. 5, p. 1, doi. 10.1371/journal.pone.0005525
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FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.
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- Journal of Computational Chemistry, 2020, v. 41, n. 9, p. 958, doi. 10.1002/jcc.26138
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- Article
Improved Modeling of Cation‐π and Anion‐Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.
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- Journal of Computational Chemistry, 2020, v. 41, n. 5, p. 439, doi. 10.1002/jcc.26067
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- Article
Polarizable force field for RNA based on the classical drude oscillator.
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- Journal of Computational Chemistry, 2018, v. 39, n. 32, p. 2624, doi. 10.1002/jcc.25709
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Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model.
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- Journal of Computational Chemistry, 2018, v. 39, n. 22, p. 1707, doi. 10.1002/jcc.25345
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Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.
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- Journal of Computational Chemistry, 2018, v. 39, n. 21, p. 1682, doi. 10.1002/jcc.25339
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- Article
Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches.
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- Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1238, doi. 10.1002/jcc.24522
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CHARMM-GUI 10 years for biomolecular modeling and simulation.
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- Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1114, doi. 10.1002/jcc.24660
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- Article
Additive CHARMM Force Field for Naturally Occurring Modified Ribonucleotides.
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- Journal of Computational Chemistry, 2016, v. 37, n. 9/10, p. 896, doi. 10.1002/jcc.24307
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- Article
DIRECT-ID: An automated method to identify and quantify conformational variations-application to β<sub>2</sub>-adrenergic GPCR.
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- Journal of Computational Chemistry, 2016, v. 37, n. 4, p. 416, doi. 10.1002/jcc.24231
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- Article
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
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- Journal of Computational Chemistry, 2015, v. 36, n. 19, p. 1473, doi. 10.1002/jcc.23937
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- Article
Robustness in the fitting of molecular mechanics parameters.
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- Journal of Computational Chemistry, 2015, v. 36, n. 14, p. 1083, doi. 10.1002/jcc.23897
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Robustness in the Fitting of Molecular Mechanics Parameters.
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- Journal of Computational Chemistry, 2015, v. 36, n. 8, p. 1083, doi. 10.1002/jcc.23897
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- Article
All-atom polarizable force field for DNA based on the classical drude oscillator model.
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- Journal of Computational Chemistry, 2014, v. 35, n. 16, p. 1219, doi. 10.1002/jcc.23611
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CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
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- Journal of Computational Chemistry, 2013, v. 34, n. 25, p. 2135, doi. 10.1002/jcc.23354
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- Article
(Ala)<sub>4</sub>-X-(Ala)<sub>4</sub> as a model system for the optimization of the χ<sub>1</sub> and χ<sub>2</sub> amino acid side-chain dihedral empirical force field parameters.
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- Journal of Computational Chemistry, 2013, v. 34, n. 7, p. 593, doi. 10.1002/jcc.23178
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Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations.
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- Journal of Computational Chemistry, 2012, v. 33, n. 31, p. 2451, doi. 10.1002/jcc.23067
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Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery.
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- Journal of Computational Chemistry, 2012, v. 33, n. 23, p. 1880, doi. 10.1002/jcc.23026
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Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications.
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- Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2009, v. 124, n. 1/2, p. 11, doi. 10.1007/s00214-009-0617-x
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- Article
Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae.
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- PLoS ONE, 2021, v. 16, n. 1, p. 1, doi. 10.1371/journal.pone.0244967
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- Article