R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. - Wikidata - wikimedia - TriplyDB

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

http://www.wikidata.org/entity/Q31014950

about

A systematic framework for molecular dynamics simulations of protein post-translational modifications Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy The Closing Mechanism of DNA Polymerase I at Atomic Resolution Aurone synthase is a catechol oxidase with hydroxylase activity and provides insights into the mechanism of plant polyphenol oxidases.Structural Basis for Autoinhibition of CTP:Phosphocholine Cytidylyltransferase (CCT), the Regulatory Enzyme in Phosphatidylcholine Synthesis, by Its Membrane-binding Amphipathic Helix Specificity of a UDP-GalNAc pyranose-furanose mutase: a potential therapeutic target for Campylobacter jejuni infections Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces Designed abscisic acid analogs as antagonists of PYL-PP2C receptor interactions Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics Molecular dynamics of CYP2D6 polymorphisms in the absence and presence of a mechanism-based inactivator reveals changes in local flexibility and dominant substrate access channels Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations Structure-based inhibition of protein-protein interactions.Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr(215) in Aerococcus viridans lactate oxidase.Synthesis, Physicochemical Studies, Molecular Dynamics Simulations, and Metal-Ion-Dependent Antiproliferative and Antiangiogenic Properties of Cone ICL670-Substituted Calix[4]arenes USP15 regulates SMURF2 kinetics through C-lobe mediated deubiquitination.Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics Competitive solvent-molecule interactions govern primary processes of diphenylcarbene in solvent mixtures Synthesis and characterization of a new photoinduced switchable β-cyclodextrin dimer.Evaluation of Acridine Orange Derivatives as DNA-Targeted Radiopharmaceuticals for Auger Therapy: Influence of the Radionuclide and Distance to DNA Protein post-translational modifications: In silico prediction tools and molecular modeling.Targeting YAP/TAZ-TEAD protein-protein interactions using fragment-based and computational modeling approaches.Origin, diversification and substrate specificity in the family of NCS1/FUR transporters.Structural basis of single molecular heparin-FX06 interaction revealed by SPM measurements and molecular simulations.Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model Reduced curvature of ligand-binding domain free-energy surface underlies partial agonism at NMDA receptors.Allosteric regulation of focal adhesion kinase by PIP₂ and ATP.Dynamics of CYP51: implications for function and inhibitor design.Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2.A consistent force field parameter set for zwitterionic amino acid residues.Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation Indolo[3,2-c]quinoline G-quadruplex stabilizers: a structural analysis of binding to the human telomeric G-quadruplex.A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers.The Augmenting Effects of Desolvation and Conformational Energy Terms on the Predictions of Docking Programs against mPGES-1.Enantioselective Benzylic Hydroxylation Catalysed by P450 Monooxygenases: Characterisation of a P450cam Mutant Library and Molecular Modelling.Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase.Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).

P2860

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P2860

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

http://www.wikidata.org/entity/Q31014950

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2011 nî lūn-bûn

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2011 թուականի Մայիսին հրատարակուած գիտական յօդուած

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2011 թվականի մայիսին հրատարակված գիտական հոդված

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2011年の論文

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2011年学术文章

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2011年学术文章

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2011年学术文章

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2011年学术文章

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2011年学术文章

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2011年學術文章

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R.E.D. Server: a web service f ...... cules and molecular fragments.

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Elodie Garcia

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Enguerran Vanquelef

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François-Yves Dupradeau

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Gaelle Marquant

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Geoffroy Klimerak

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Jean Charles Delepine

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Piotr Cieplak

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Sabrina Simon

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P2860

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

The Amber biomolecular simulation programs

Comparison of multiple Amber force fields and development of improved protein backbone parameters

R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Development and testing of a general amber force field

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

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10.1093/NAR/GKR288

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Web Server issue

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39

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2011-05-23T00:00:00Z

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