(Q27657572)

2

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Ken A. Dill

5

object named as

Ken A Dill

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author name string

Sarah E Boyce

1

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Alan P Graves

4

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Brian K Shoichet

Journal of Molecular Biology

6

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language of work or name

English

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publication date

11 December 2009

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published in

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volume

394

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issue

4

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page(s)

747-63

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cites work

DOCK 6: combining techniques to model RNA-small molecule complexes

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Predicting absolute ligand binding free energies to a simple model site

20 March 2017

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A model binding site for testing scoring functions in molecular docking

20 March 2017

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Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

20 March 2017

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GROMACS: fast, flexible, and free

20 March 2017

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Coot: model-building tools for molecular graphics

20 March 2017

1 reference

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Refinement of macromolecular structures by the maximum-likelihood method

20 March 2017

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PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

20 March 2017

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Automatic atom type and bond type perception in molecular mechanical calculations

20 March 2017

1 reference

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Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

7 April 2017

1 reference

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Host-guest complexes with protein-ligand-like affinities: computational analysis and design

29 September 2017

1 reference

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The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

29 September 2017

1 reference

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Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution

29 September 2017

1 reference

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Predicting small-molecule solvation free energies: an informal blind test for computational chemistry

29 September 2017

1 reference

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A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation

29 September 2017

1 reference

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Accurate and efficient corrections for missing dispersion interactions in molecular simulations

29 September 2017

1 reference

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Development and validation of a modular, extensible docking program: DOCK 5.

29 September 2017

1 reference

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Modeling electrostatic effects in proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Testing a flexible-receptor docking algorithm in a model binding site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Molecular complexity and its impact on the probability of finding leads for drug discovery

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Second-site revertants of an inactive T4 lysozyme mutant restore activity by restructuring the active site cleft

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

A new ultrasensitive scanning calorimeter.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Predictions of hydration free energies from all-atom molecular dynamics simulations.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2788029

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

27 November 2018

1 reference

12 December 2020

FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

1 reference

12 December 2020

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

1 reference

12 December 2020

Processing of X-ray diffraction data collected in oscillation mode

1 reference

12 December 2020

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

12 December 2020