Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. (Q52141704)

23 April 2018

title

Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. (English)

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23 April 2018

author name string

J Marelius

1

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23 April 2018

K Kolmodin

2

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23 April 2018

I Feierberg

3

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23 April 2018

J Aqvist

4

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23 April 2018

publication date

1 August 1998

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23 April 2018

Journal of Molecular Graphics & Modelling

published in

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23 April 2018

volume

16

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23 April 2018

page(s)

213-25, 261

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23 April 2018

issue

4-6

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23 April 2018

Free energy via molecular simulation: applications to chemical and biomolecular systems

cites work

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

A new method for predicting binding affinity in computer-aided drug design

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Ligand binding affinity prediction by linear interaction energy methods

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

A new method for predicting binding free energy between receptor and ligand.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

An approximate but efficient method to calculate free energy trends by computer simulation: application to dihydrofolate reductase-inhibitor complexes.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Binding free energy calculations for P450cam-substrate complexes

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Molecular dynamics simulations of the docking of substituted N5-deazapterins to dihydrofolate reductase

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Molecular dynamics with coupling to an external bath

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Protein tyrosine phosphatases: a diverse family of intracellular and transmembrane enzymes

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Protein tyrosine phosphatases take off.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

The role of Cys12, Cys17 and Arg18 in the catalytic mechanism of low-M(r) cytosolic phosphotyrosine protein phosphatase

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Energetics of nucleophile activation in a protein tyrosine phosphatase

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Crystal structure of bovine low molecular weight phosphotyrosyl phosphatase complexed with the transition state analog vanadate

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Roles of aspartic acid-181 and serine-222 in intermediate formation and hydrolysis of the mammalian protein-tyrosine-phosphatase PTP1

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

Electrostatic evaluation of the signature motif (H/V)CX5R(S/T) in protein-tyrosine phosphatases.

1 reference

https://api.crossref.org/works/10.1016%2FS1093-3263%2898%2980006-5

7 January 2021

10.1016/S1093-3263(98)80006-5

Identifiers

DOI

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23 April 2018

PubMed ID

10522241

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23 April 2018