(Q39676629)

13 September 2017

title

Molecular simulation methods in drug discovery: a prospective outlook (English)

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13 September 2017

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Xavier Barril

1

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13 September 2017

F Javier Luque

series ordinal

2

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13 September 2017

publication date

8 December 2011

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Journal of Computer - Aided Molecular Design

13 September 2017

published in

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13 September 2017

volume

26

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13 September 2017

issue

1

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13 September 2017

page(s)

81-86

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Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

13 September 2017

cites work

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

The many roles of computation in drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Accelerating molecular modeling applications with graphics processors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Inhibitors of serine proteases as potential therapeutic agents: the road from thrombin to tryptase to cathepsin G.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

2009 Edward E Smissman Award. Pharmaceutical "gold" from neurostabilizing agents: topiramate and successor molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Protein flexibility and ligand recognition: challenges for molecular modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Combining docking and molecular dynamic simulations in drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Modified replica exchange simulation methods for local structure refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Coarse-grained models for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Improved sampling methods for molecular simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Single-molecule pulling simulations can discern active from inactive enzyme inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Molecular motions in drug design: the coming age of the metadynamics method

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

The druggable genome: an update

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

How many drug targets are there?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Druggability indices for protein targets derived from NMR-based screening data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Structure-based maximal affinity model predicts small-molecule druggability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Understanding and predicting druggability. A high-throughput method for detection of drug binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A medicinal chemist's guide to molecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A review of protein-small molecule docking methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Ligand docking and structure-based virtual screening in drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A critical assessment of docking programs and scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Investigation of MM-PBSA rescoring of docking poses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

An improved method to predict the entropy term with the MM/PBSA approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE).

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Efficient drug lead discovery and optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Current status of the AMOEBA polarizable force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A quantum mechanical polarizable force field for biomolecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Accurate Induction Energies for Small Organic Molecules: 1. Theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Ligand Affinities Estimated by Quantum Chemical Calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Is quantum mechanics necessary for predicting binding free energy?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9506-1

Acceleration of a QM/MM-QMC simulation using GPU

21 January 2018

1 reference

12 December 2020

Pyrano[3,2-c]quinoline-6-chlorotacrine hybrids as a novel family of acetylcholinesterase- and beta-amyloid-directed anti-Alzheimer compounds

1 reference

12 December 2020

Critical review of the role of HTS in drug discovery

1 reference

12 December 2020

Toward a Separate Reproduction of the Contributions to the Hartree-Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential

1 reference

12 December 2020

Flexible docking in solution using metadynamics

1 reference

12 December 2020

Surviving the blockbuster syndrome

1 reference

12 December 2020

Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs).

1 reference

12 December 2020

Shielded hydrogen bonds as structural determinants of binding kinetics: application in drug design

1 reference

12 December 2020

Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox

1 reference

12 December 2020

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

1 reference

12 December 2020

Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring

1 reference

12 December 2020

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.

1 reference

12 December 2020

Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes

1 reference

12 December 2020

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

1 reference

12 December 2020

Quantum mechanical polarizable force field (QMPFF3): refinement and validation of the dispersion interaction for aromatic carbon

1 reference

12 December 2020

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations

1 reference

12 December 2020

10.1007/S10822-011-9506-1

Identifiers

DOI

1 reference

13 September 2017

DBLP publication ID

journals/jcamd/BarrilL12

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DBLP Dataset 2021-01-02

28 January 2021

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