Virtual screening using molecular simulations (Q34975702)

5 August 2017

Virtual screening using molecular simulations (English)

1 reference

5 August 2017

1 reference

Ray Luo

5

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author name string

Tianyi Yang

1

1 reference

5 August 2017

Johnny C Wu

2

1 reference

5 August 2017

Chunli Yan

3

1 reference

5 August 2017

Yuanfeng Wang

4

1 reference

5 August 2017

Michael B Gonzales

6

1 reference

5 August 2017

Kevin N Dalby

7

1 reference

5 August 2017

Pengyu Ren

8

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5 August 2017

language of work or name

English

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publication date

12 April 2011

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5 August 2017

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5 August 2017

79

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5 August 2017

6

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5 August 2017

1940-1951

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Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum

5 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

How to improve R&D productivity: the pharmaceutical industry's grand challenge

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Current status of the AMOEBA polarizable force field

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Theory of free energy and entropy in noncovalent binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Efficient drug lead discovery and optimization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Molecular docking and ligand specificity in fragment-based inhibitor discovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Very fast prediction and rationalization of pKa values for protein-ligand complexes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Recent developments in fragment-based drug discovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Calculation of protein-ligand binding free energy by using a polarizable potential

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Binding MOAD, a high-quality protein-ligand database.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Calculation of protein-ligand binding affinities.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

8 July 2018

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

A critical assessment of docking programs and scoring functions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Empirical correlation between hydrophobic free energy and aqueous cavity surface area

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Topical dorzolamide for the treatment of cystoid macular edema in patients with retinitis pigmentosa

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Automatic atom type and bond type perception in molecular mechanical calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

The Amber biomolecular simulation programs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Computer-based de novo design of drug-like molecules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

The PDBbind database: methodologies and updates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Development and testing of a general amber force field

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Exploring protein native states and large-scale conformational changes with a modified generalized born model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

The many roles of computation in drug discovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Modeller: generation and refinement of homology-based protein structure models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Specific targeted therapy of chronic myelogenous leukemia with imatinib

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Effective Born radii in the generalized Born approximation: the importance of being perfect

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Functional genomics and target validation approaches using antisense oligonucleotide technology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

What are the dielectric "constants" of proteins and how to validate electrostatic models?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Detailed analysis of scoring functions for virtual screening

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Screening for human ADME/Tox drug properties in drug discovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Rational design of potent sialidase-based inhibitors of influenza virus replication

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Application of the three-dimensional structures of protein target molecules in structure-based drug design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Langevin modes of macromolecules: applications to crambin and DNA hexamers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Comparative evaluation of 11 scoring functions for molecular docking

8 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Drug discovery: Pulled from a protein's embrace

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Large-scale application of high-throughput molecular mechanics with Poisson-Boltzmann surface area for routine physics-based scoring of protein-ligand complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Analytical molecular surface calculation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Correlating solvation free energies and surface tensions of hydrocarbon solutes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

How to obtain statistically converged MM/GBSA results.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3092865

Molecular dynamics with coupling to an external bath

26 October 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23018

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

21 January 2018

1 reference

12 December 2020

Binding MOAD (Mother Of All Databases)

1 reference

12 December 2020

Thermodynamic analysis of binding of p-substituted benzamidines to trypsin

1 reference

12 December 2020

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

1 reference

12 December 2020

Dynamic combinatorial chemistry

1 reference

12 December 2020

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.23018

1 reference

5 August 2017

1 reference

5 August 2017

1 reference