DOCK 6: Impact of new features and current docking performance (Q35748554)

10 August 2017

title

DOCK 6: Impact of new features and current docking performance (English)

1 reference

10 August 2017

7

David A Case

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author name string

William J Allen

1

1 reference

10 August 2017

Trent E Balius

2

1 reference

10 August 2017

Sudipto Mukherjee

3

1 reference

10 August 2017

Scott R Brozell

4

1 reference

10 August 2017

Demetri T Moustakas

5

1 reference

10 August 2017

P Therese Lang

6

1 reference

10 August 2017

David A Case

7

1 reference

10 August 2017

Irwin D Kuntz

8

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10 August 2017

Robert C Rizzo

9

1 reference

10 August 2017

language of work or name

1 reference

1 June 2015

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Journal of Computational Chemistry

10 August 2017

published in

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10 August 2017

volume

36

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10 August 2017

issue

15

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10 August 2017

page(s)

1132-1156

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Pharmacophore-based similarity scoring for DOCK

10 August 2017

cites work

1 reference

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12 July 2018

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12 July 2018

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Effect of mutations at position E138 in HIV-1 reverse transcriptase and their interactions with the M184I mutation on defining patterns of resistance to nonnucleoside reverse transcriptase inhibitors rilpivirine and etravirine

12 July 2018

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12 July 2018

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12 July 2018

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Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41

12 July 2018

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12 July 2018

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Targeting fatty acid binding protein (FABP) anandamide transporters - a novel strategy for development of anti-inflammatory and anti-nociceptive drugs

12 July 2018

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A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

12 July 2018

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Protein flexibility in virtual screening: the BACE-1 case study

12 July 2018

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ALiBERO: evolving a team of complementary pocket conformations rather than a single leader

12 July 2018

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Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking

12 July 2018

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ZINC: a free tool to discover chemistry for biology

12 July 2018

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Evaluation of DOCK 6 as a pose generation and database enrichment tool

12 July 2018

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Surflex-Dock: Docking benchmarks and real-world application

12 July 2018

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Footprint-based identification of viral entry inhibitors targeting HIVgp41.

12 July 2018

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Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor

12 July 2018

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A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking

12 July 2018

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Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

12 July 2018

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Identification of inhibitors against Mycobacterium tuberculosis thiamin phosphate synthase, an important target for the development of anti-TB drugs

12 July 2018

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Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the “Hydrophobic Wall” of Carbonic Anhydrase

12 July 2018

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Systematic placement of structural water molecules for improved scoring of protein-ligand interactions

12 July 2018

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Small molecule inhibitors of SHP2 tyrosine phosphatase discovered by virtual screening

12 July 2018

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Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons

12 July 2018

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FRED pose prediction and virtual screening accuracy

12 July 2018

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12 July 2018

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Computer-aided drug-discovery techniques that account for receptor flexibility

12 July 2018

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HIV-1 protease mutations and protease inhibitor cross-resistance

12 July 2018

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Lersivirine, a Nonnucleoside Reverse Transcriptase Inhibitor with Activity against Drug-Resistant Human Immunodeficiency Virus Type 1

12 July 2018

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Origins of resistance to the HIVgp41 viral entry inhibitor T20.

12 July 2018

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Current status of the AMOEBA polarizable force field

12 July 2018

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TMC278, a next-generation nonnucleoside reverse transcriptase inhibitor (NNRTI), active against wild-type and NNRTI-resistant HIV-1.

12 July 2018

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The impact of individual human immunodeficiency virus type 1 protease mutations on drug susceptibility is highly influenced by complex interactions with the background protease sequence

12 July 2018

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

12 July 2018

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Docking for fragment inhibitors of AmpC -lactamase

12 July 2018

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

12 July 2018

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

12 July 2018

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Design and biological evaluation of novel, balanced dual PPARalpha/gamma agonists

12 July 2018

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Exploiting ordered waters in molecular docking

12 July 2018

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Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors

12 July 2018

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4-Amino-6-arylamino-pyrimidine-5-carbaldehyde hydrazones as potent ErbB-2/EGFR dual kinase inhibitors

12 July 2018

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Thermodynamic and structure guided design of statin based inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A reductase

12 July 2018

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Discovery of novel 4-amino-6-arylaminopyrimidine-5-carbaldehyde oximes as dual inhibitors of EGFR and ErbB-2 protein tyrosine kinases

12 July 2018

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Flexible ligand docking to multiple receptor conformations: a practical alternative

12 July 2018

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

12 July 2018

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Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

12 July 2018

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High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations

12 July 2018

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Structure-based activity prediction for an enzyme of unknown function

12 July 2018

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Predicting absolute ligand binding free energies to a simple model site

12 July 2018

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Relationship of potency and resilience to drug resistant mutations for GW420867X revealed by crystal structures of inhibitor complexes for wild-type, Leu100Ile, Lys101Glu, and Tyr188Cys mutant HIV-1 reverse transcriptases

12 July 2018

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Structures of Lung Cancer-Derived EGFR Mutants and Inhibitor Complexes: Mechanism of Activation and Insights into Differential Inhibitor Sensitivity

12 July 2018

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Discovery and initial SAR of 3-(1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-ones as inhibitors of insulin-like growth factor 1-receptor (IGF-1R)

12 July 2018

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Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

12 July 2018

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Benchmarking sets for molecular docking

12 July 2018

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

12 July 2018

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eHiTS: an innovative approach to the docking and scoring function problems.

12 July 2018

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

12 July 2018

1 reference

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

12 July 2018

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The Amber biomolecular simulation programs

12 July 2018

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12 July 2018

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

12 July 2018

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Virtual screening of chemical libraries

12 July 2018

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Soft docking and multiple receptor conformations in virtual screening

12 July 2018

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A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells

12 July 2018

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

12 July 2018

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Development and testing of a general amber force field

12 July 2018

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Estrogen receptor ligands. II. Discovery of benzoxathiins as potent, selective estrogen receptor alpha modulators

12 July 2018

1 reference

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The many roles of computation in drug discovery

12 July 2018

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Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

12 July 2018

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Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

12 July 2018

1 reference

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Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

12 July 2018

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Improved protein-ligand docking using GOLD

12 July 2018

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

12 July 2018

1 reference

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A model binding site for testing scoring functions in molecular docking

12 July 2018

1 reference

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Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor

12 July 2018

1 reference

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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

12 July 2018

1 reference

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Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations

12 July 2018

1 reference

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Analysis of inhibitor binding in influenza virus neuraminidase

12 July 2018

1 reference

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Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin-biotin system

12 July 2018

1 reference

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12 July 2018

The Protein Data Bank

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Structural analysis of inhibitor binding to human carbonic anhydrase II

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Crystallographic analysis of human immunodeficiency virus 1 protease with an analog of the conserved CA-p2 substrate -- interactions with frequently occurring glutamic acid residue at P2' position of substrates

12 July 2018

1 reference

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Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents

12 July 2018

1 reference

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Structure-based discovery of inhibitors of thymidylate synthase

12 July 2018

1 reference

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Drug-protein interactions. Refined structures of three sulfonamide drug complexes of human carbonic anhydrase I enzyme

12 July 2018

1 reference

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

A geometric approach to macromolecule-ligand interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Structural origins of high-affinity biotin binding to streptavidin

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Protein docking and complementarity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Structure-based strategies for drug design and discovery

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Distinct resistance patterns to etravirine and rilpivirine in viruses containing nonnucleoside reverse transcriptase inhibitor mutations at baseline

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

A water-based mechanism of specificity and resistance for lapatinib with ErbB family kinases

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Genotypic resistance profiles associated with virological failure to darunavir-containing regimens: a cross-sectional analysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Molecular docking with ligand attached water molecules.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Differential impact of the HIV-1 non-nucleoside reverse transcriptase inhibitor mutations K103N and M230L on viral replication and enzyme function

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Pattern and impact of emerging resistance mutations in treatment experienced patients failing darunavir-containing regimen.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Diverse, high-quality test set for the validation of protein-ligand docking performance.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Modeling water molecules in protein-ligand docking using GOLD.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Virtual screening against metalloenzymes for inhibitors and substrates

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Resistance to nevirapine of HIV-1 reverse transcriptase mutants: loss of stabilizing interactions and thermodynamic or steric barriers are induced by different single amino acid substitutions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

A fast flexible docking method using an incremental construction algorithm.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4469538

Molecular docking using shape descriptors

25 September 2018

1 reference

Automated docking with grid-based energy evaluation

21 January 2018

1 reference

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

21 January 2018

1 reference

Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects

21 January 2018

1 reference

New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions

21 January 2018

1 reference

The Hungarian method for the assignment problem

21 January 2018

1 reference

Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138

21 January 2018

1 reference

12 December 2020

Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4

1 reference

12 December 2020

A call to arms: what you can do for computational drug discovery

1 reference

12 December 2020

An old target revisited: two new privileged skeletons and an unexpected binding mode for HIV-protease inhibitors

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.23905

1 reference

journals/jcc/AllenBMBMLCKR15

10 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

10 August 2017

1 reference