(Q27649874)

1

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Devleena M Shivakumar

2

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Sarah E Boyce

3

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David A Case

5

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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

28 March 2008

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published in

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volume

377

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page(s)

914-34

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issue

3

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cites work

Prediction and assignment of function for a divergent N-succinyl amino acid racemase

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Predicting absolute ligand binding free energies to a simple model site

20 March 2017

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ZINC--a free database of commercially available compounds for virtual screening

20 March 2017

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A model binding site for testing scoring functions in molecular docking

20 March 2017

1 reference

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Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase

20 March 2017

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Combinatorial computational method gives new picomolar ligands for a known enzyme

20 March 2017

1 reference

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Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein

20 March 2017

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Flexible ligand docking using conformational ensembles

20 March 2017

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Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Coot: model-building tools for molecular graphics

20 March 2017

1 reference

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The CCP4 suite: programs for protein crystallography

20 March 2017

1 reference

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Development and testing of a general amber force field

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Automatic atom type and bond type perception in molecular mechanical calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

A hierarchical approach to all-atom protein loop prediction

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Probing molecular docking in a charged 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=2752715

In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Experimental screening of dihydrofolate reductase yields a "test set" of 50,000 small molecules for a computational data-mining and docking competition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

A low-molecular-weight compound discovered through virtual database screening inhibits Stat3 function in breast cancer cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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=2752715

How does consensus scoring work for virtual library screening? An idealized computer experiment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

FlexE: efficient molecular docking considering protein structure variations.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Statistical potentials and scoring functions applied to protein-ligand binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Detailed analysis of scoring functions for virtual screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

A computer screening approach to immunoglobulin superfamily structures and interactions: discovery of small non-peptidic CD4 inhibitors as novel immunotherapeutics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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=2752715

Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2752715

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

27 November 2018

1 reference

12 December 2020

Minimizing false positives in kinase virtual screens

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

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

1 reference

12 December 2020

Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring

1 reference

12 December 2020

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes

1 reference

12 December 2020

Processing of X-ray diffraction data collected in oscillation mode

1 reference

12 December 2020

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

1 reference

12 December 2020

10.1016/J.JMB.2008.01.049

Identifiers

DOI

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3785108

3785108

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1 reference

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