(Q33521726)

27 July 2017

title

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

1 reference

27 July 2017

1 reference

Jennifer L Knight

1

1 reference

27 July 2017

Charles L Brooks

series ordinal

2

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27 July 2017

publication date

1 January 2009

1 reference

Journal of Chemical Theory and Computation

27 July 2017

published in

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27 July 2017

volume

5

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27 July 2017

issue

6

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27 July 2017

page(s)

1680-1691

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

27 July 2017

cites work

1 reference

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

21 June 2018

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Current topics in computer-aided drug design

21 June 2018

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21 June 2018

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21 June 2018

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Calculation of protein-ligand binding affinities.

21 June 2018

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Towards predictive ligand design with free-energy based computational methods?

21 June 2018

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Automatic atom type and bond type perception in molecular mechanical calculations

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Empirical force fields for biological macromolecules: overview and issues.

21 June 2018

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21 June 2018

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The many roles of computation in drug discovery

21 June 2018

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Force fields for protein simulations

21 June 2018

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Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method

21 June 2018

1 reference

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Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant

21 June 2018

1 reference

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Synthesis and anti-HIV-1 activity of 4,5,6,7-tetrahydro-5-methylimidazo-[4,5,1-jk][1,4]benzodiazepin- 2(1H)-one (TlBO) derivatives. 4.

21 June 2018

1 reference

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Classical electrostatics in biology and chemistry

21 June 2018

1 reference

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Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

21 June 2018

1 reference

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Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

21 June 2018

1 reference

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Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA.

31 October 2018

1 reference

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Accuracy of free energies of hydration using CM1 and CM3 atomic charges

31 October 2018

1 reference

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New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

31 October 2018

1 reference

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Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719862

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719862

Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20046995

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20046995

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Polarizable Force Fields: History, Test Cases, and Prospects

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20046995

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT900079T

1 reference

27 July 2017

1 reference

27 July 2017

1 reference