Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. - Wikidata - awgldk - TriplyDB

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.

http://www.wikidata.org/entity/Q37364377

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Biomolecular electrostatics and solvation: a computational perspective The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site Force Field for Peptides and Proteins based on the Classical Drude Oscillator Alchemical free energy methods for drug discovery: progress and challenges Current status of the AMOEBA polarizable force field The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases Trypsin-ligand binding free energy calculation with AMOEBA.Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.Molecular dynamics simulations and drug discovery From laptop to benchtop to bedside: structure-based drug design on protein targets.Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field.POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1.Multipole electrostatics in hydration free energy calculations.Virtual screening using molecular simulations.Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone.Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study.Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations.Computational studies of difference in binding modes of peptide and non-peptide inhibitors to MDM2/MDMX based on molecular dynamics simulations.Automation of AMOEBA polarizable force field parameterization for small molecules Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential.Recent theoretical and computational advances for modeling protein-ligand binding affinities Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation Separated topologies--a method for relative binding free energy calculations using orientational restraints.Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues Classical electrostatics for biomolecular simulations.Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations.Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.Limiting assumptions in molecular modeling: electrostatics.Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport.Current and emerging opportunities for molecular simulations in structure-based drug design.Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

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P2860

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.

http://www.wikidata.org/entity/Q37364377

description

article científic

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article scientifique

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articolo scientifico

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artigo científico

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bilimsel makale

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scientific article published on August 2009

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vedecký článok

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vetenskaplig artikel

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videnskabelig artikel

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name

Trypsin-ligand binding free en ...... ns with polarizable potential.

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Trypsin-ligand binding free en ...... ns with polarizable potential.

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Trypsin-ligand binding free en ...... ns with polarizable potential.

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Trypsin-ligand binding free en ...... ns with polarizable potential.

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Journal of Computational Chemistry

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Trypsin-ligand binding free en ...... ns with polarizable potential.

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Dian Jiao

http://www.w3.org/2001/XMLSchema#string

Guohui Li

http://www.w3.org/2001/XMLSchema#string

Jiajing Zhang

http://www.w3.org/2001/XMLSchema#string

Michael J Schnieders

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Pengyu Ren

http://www.w3.org/2001/XMLSchema#string

Robert E Duke

http://www.w3.org/2001/XMLSchema#string

P2860

Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements

Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine

A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site

Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

Molecular dynamics simulations of biomolecules: long-range electrostatic effects.

Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies.

P304

1701-1711

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scholarly article

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10.1002/JCC.21268

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11

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30

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19399779

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2752704

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