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Decoys for docking
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scholarly article
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
title
Decoys for docking
(English)
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
author
Ruth Brenk
object named as
Ruth Brenk
series ordinal
2
0 references
author name string
Alan P Graves
series ordinal
1
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
Brian K Shoichet
series ordinal
3
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
language of work or name
English
0 references
publication date
1 June 2005
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
published in
Journal of Medicinal Chemistry
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
volume
48
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
page(s)
3714-3728
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
issue
11
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
cites work
UCSF Chimera--a visualization system for exploratory research and analysis
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3 June 2018
Testing a flexible-receptor docking algorithm in a model binding site
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PubMed Central
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3 June 2018
Combination of scoring functions improves discrimination in protein-protein docking.
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PubMed Central
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3 June 2018
A specific mechanism of nonspecific inhibition
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3 June 2018
A model binding site for testing scoring functions in molecular docking
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PubMed Central
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3 June 2018
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
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3 June 2018
Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase
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3 June 2018
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.
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PubMed Central
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3 June 2018
A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening
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PubMed Central
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3 June 2018
PRO_SELECT: combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors
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PubMed Central
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3 June 2018
Combinatorial computational method gives new picomolar ligands for a known enzyme
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3 June 2018
Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design
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3 June 2018
Discovery of small-molecule inhibitors of Bcl-2 through structure-based computer screening
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3 June 2018
High-throughput docking for lead generation
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PubMed Central
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3 June 2018
Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis.
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PubMed Central
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3 June 2018
Detailed analysis of scoring functions for virtual screening
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PubMed Central
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3 June 2018
A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase
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PubMed Central
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3 June 2018
Deciphering common failures in molecular docking of ligand-protein complexes.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
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3 June 2018
How to generate improved potentials for protein tertiary structure prediction: a lattice model study.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Ab initio protein structure prediction of CASP III targets using ROSETTA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
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3 June 2018
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
1 reference
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PubMed Central
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3 June 2018
Flexible ligand docking using conformational ensembles
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
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3 June 2018
Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
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3 June 2018
Modelling protein docking using shape complementarity, electrostatics and biochemical information
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PubMed Central
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3 June 2018
How to derive a protein folding potential? A new approach to an old problem
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
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3 June 2018
Energy functions that discriminate X-ray and near native folds from well-constructed decoys
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
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3 June 2018
A geometric approach to macromolecule-ligand interactions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
Evaluation of protein models by atomic solvation preference.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
3 June 2018
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Assessing scoring functions for protein-ligand interactions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Comparative evaluation of 11 scoring functions for molecular docking
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
MOPED: method for optimizing physical energy parameters using decoys.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Scoring docked conformations generated by rigid-body protein-protein docking.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
The discovery of steroids and other novel FKBP inhibitors using a molecular docking program
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
A general and fast scoring function for protein-ligand interactions: a simplified potential approach.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
A fast flexible docking method using an incremental construction algorithm.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Matching chemistry and shape in molecular docking
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646
retrieved
26 November 2018
Distance-dependent, pair potential for protein folding: results from linear optimization
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15916423
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Protein-protein docking. Generation and filtering of complexes
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15916423
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Protein docking using continuum electrostatics and geometric fit
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15916423
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Processing of X-ray diffraction data collected in oscillation mode
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15916423
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15916423
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1021/JM0491187
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
PMCID
1557646
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
PubMed ID
15916423
1 reference
stated in
Europe PubMed Central
PMCID
1557646
retrieved
13 October 2017
ResearchGate publication ID
7826230
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