Decoys for docking (Q30350781)

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Language	Label	Description	Also known as
English	Decoys for docking	scientific article

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scholarly article

1 reference

Europe PubMed Central

13 October 2017

Decoys for docking (English)

1 reference

Europe PubMed Central

13 October 2017

object named as

Ruth Brenk

2

0 references

author name string

Alan P Graves

1

1 reference

Europe PubMed Central

13 October 2017

Brian K Shoichet

3

1 reference

Europe PubMed Central

13 October 2017

language of work or name

0 references

publication date

1 June 2005

1 reference

Europe PubMed Central

13 October 2017

Journal of Medicinal Chemistry

1 reference

Europe PubMed Central

13 October 2017

48

1 reference

Europe PubMed Central

13 October 2017

3714-3728

1 reference

Europe PubMed Central

13 October 2017

11

1 reference

Europe PubMed Central

13 October 2017

UCSF Chimera--a visualization system for exploratory research and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Combination of scoring functions improves discrimination in protein-protein docking.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A specific mechanism of nonspecific inhibition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A model binding site for testing scoring functions in molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Combinatorial computational method gives new picomolar ligands for a known enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Discovery of small-molecule inhibitors of Bcl-2 through structure-based computer screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

High-throughput docking for lead generation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Detailed analysis of scoring functions for virtual screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Deciphering common failures in molecular docking of ligand-protein complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

How to generate improved potentials for protein tertiary structure prediction: a lattice model study.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Ab initio protein structure prediction of CASP III targets using ROSETTA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Flexible ligand docking using conformational ensembles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Modelling protein docking using shape complementarity, electrostatics and biochemical information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

How to derive a protein folding potential? A new approach to an old problem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A geometric approach to macromolecule-ligand interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

Evaluation of protein models by atomic solvation preference.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

3 June 2018

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Assessing scoring functions for protein-ligand interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Comparative evaluation of 11 scoring functions for molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

MOPED: method for optimizing physical energy parameters using decoys.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

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

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Scoring docked conformations generated by rigid-body protein-protein docking.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

The discovery of steroids and other novel FKBP inhibitors using a molecular docking program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

A fast flexible docking method using an incremental construction algorithm.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Matching chemistry and shape in molecular docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1557646

26 November 2018

Distance-dependent, pair potential for protein folding: results from linear optimization

1 reference

https://pubmed.ncbi.nlm.nih.gov/15916423

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein-protein docking. Generation and filtering of complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/15916423

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein docking using continuum electrostatics and geometric fit

1 reference

https://pubmed.ncbi.nlm.nih.gov/15916423

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Processing of X-ray diffraction data collected in oscillation mode

1 reference

https://pubmed.ncbi.nlm.nih.gov/15916423

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

https://pubmed.ncbi.nlm.nih.gov/15916423

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JM0491187

1 reference

Europe PubMed Central

13 October 2017

1 reference

Europe PubMed Central

13 October 2017

1 reference

Europe PubMed Central

13 October 2017

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