Challenges and advances in computational docking: 2009 in review (Q37848281)

24 August 2017

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title

Challenges and advances in computational docking: 2009 in review (English)

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24 August 2017

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21360606

25 November 2024

Mark Agostino

2

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Elizabeth Yuriev

object named as

Elizabeth Yuriev

1

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Paul A. Ramsland

object named as

Paul A Ramsland

3

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language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21360606

25 November 2024

publication date

23 October 2010

1 reference

full work available at URL

24 August 2017

https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002/jmr.1077

1 reference

https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmr.1077

25 November 2024

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Journal of Molecular Recognition

25 November 2024

published in

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24 August 2017

volume

24

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24 August 2017

issue

2

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24 August 2017

page(s)

149-164

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Structure-based virtual ligand screening: recent success stories

24 August 2017

cites work

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21 January 2018

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Pushing structural information into the yeast interactome by high-throughput protein docking experiments

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Simultaneous prediction of protein folding and docking at high resolution

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Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.

21 January 2018

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High-resolution protein complexes from integrating genomic information with molecular simulation

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FRODOCK: a new approach for fast rotational protein-protein docking

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Computational study of the heterodimerization between mu and delta receptors

21 January 2018

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Convergence and combination of methods in protein-protein docking

21 January 2018

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Molecular docking screens using comparative models of proteins

21 January 2018

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Benchmarking sets for molecular docking

21 January 2018

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Homology modelling of the human adenosine A2B receptor based on X-ray structures of bovine rhodopsin, the beta2-adrenergic receptor and the human adenosine A2A receptor

21 January 2018

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Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking

21 January 2018

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Docking and scoring with alternative side-chain conformations

21 January 2018

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Managing protein flexibility in docking and its applications

21 January 2018

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Blind docking of pharmaceutically relevant compounds using RosettaLigand

21 January 2018

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RosettaLigand docking with full ligand and receptor flexibility

21 January 2018

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

21 January 2018

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MADAMM: a multistaged docking with an automated molecular modeling protocol

21 January 2018

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Novel procedure for modeling ligand/receptor induced fit effects.

21 January 2018

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

21 January 2018

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

21 January 2018

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Induced-fit docking studies of the active and inactive states of protein tyrosine kinases

21 January 2018

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A regulatory mechanism for RSK2 NH(2)-terminal kinase activity

21 January 2018

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Induced-fit docking approach provides insight into the binding mode and mechanism of action of HIV-1 integrase inhibitors.

21 January 2018

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Inside the Hsp90 inhibitors binding mode through induced fit docking.

21 January 2018

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Discovery of potent and reversible monoacylglycerol lipase inhibitors.

21 January 2018

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An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

21 January 2018

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Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

21 January 2018

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Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

21 January 2018

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The flexible pocketome engine for structural chemogenomics

21 January 2018

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Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

21 January 2018

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Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

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Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

21 January 2018

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Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs

21 January 2018

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A new method for the gradient-based optimization of molecular complexes

21 January 2018

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Scoring ensembles of docked protein:ligand interactions for virtual lead optimization

21 January 2018

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In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking

21 January 2018

1 reference

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

21 January 2018

1 reference

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?

21 January 2018

1 reference

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

21 January 2018

1 reference

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

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Improved protein-ligand docking using GOLD

21 January 2018

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Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

Conformational sampling for large-scale virtual screening: accuracy versus ensemble size.

21 January 2018

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Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK).

21 January 2018

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E-novo: an automated workflow for efficient structure-based lead optimization

21 January 2018

1 reference

Beyond the virtual screening paradigm: structure-based searching for new lead compounds

21 January 2018

1 reference

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

21 January 2018

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

21 January 2018

1 reference

An improved adaptive genetic algorithm for protein-ligand docking

21 January 2018

1 reference

Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results

21 January 2018

1 reference

The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening

21 January 2018

1 reference

An improved method to predict the entropy term with the MM/PBSA approach.

21 January 2018

1 reference

Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA).

21 January 2018

1 reference

Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.

21 January 2018

1 reference

Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.

21 January 2018

1 reference

An improved scoring function for suboptimal polar ligand complexes

21 January 2018

1 reference

Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems

21 January 2018

1 reference

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

21 January 2018

1 reference

Empirical scoring functions for advanced protein-ligand docking with PLANTS.

21 January 2018

1 reference

Docking ligands into flexible and solvated macromolecules. 5. Force-field-based prediction of binding affinities of ligands to proteins

21 January 2018

1 reference

Comparative evaluation of 11 scoring functions for molecular docking

21 January 2018

1 reference

How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?

21 January 2018

1 reference

QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors

21 January 2018

1 reference

Correlation between performance of QM/MM docking and simple classification of binding sites

21 January 2018

1 reference

Extension of QM/MM docking and its applications to metalloproteins

21 January 2018

1 reference

QM/QM docking method based on the variational finite localized molecular orbital approximation

21 January 2018

1 reference

Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations.

21 January 2018

1 reference

Quantum mechanical scoring for protein docking.

21 January 2018

1 reference

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

21 January 2018

1 reference

Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring

21 January 2018

1 reference

Comparative assessment of scoring functions on a diverse test set.

21 January 2018

1 reference

SeleX-CS: a new consensus scoring algorithm for hit discovery and lead optimization

21 January 2018

1 reference

An effective docking strategy for virtual screening based on multi-objective optimization algorithm

21 January 2018

1 reference

Validation of molecular docking programs for virtual screening against dihydropteroate synthase

21 January 2018

1 reference

Testing assumptions and hypotheses for rescoring success in protein-ligand docking

21 January 2018

1 reference

Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation

21 January 2018

1 reference

APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening.

21 January 2018

1 reference

Position specific interaction dependent scoring technique for virtual screening based on weighted protein--ligand interaction fingerprint profiles

21 January 2018

1 reference

Steering protein-ligand docking with quantitative NMR chemical shift perturbations

21 January 2018

1 reference

Targeted scoring functions for virtual screening

21 January 2018

1 reference

Robust optimization of scoring functions for a target class.

21 January 2018

1 reference

Docking screens: right for the right reasons?

21 January 2018

1 reference

Predicting multiple ligand binding modes using self-consistent pharmacophore hypotheses

21 January 2018

1 reference

Developing novel approaches to improve binding energy estimation and virtual screening: a PARP case study

21 January 2018

1 reference

In silico analysis of antibody-carbohydrate interactions and its application to xenoreactive antibodies

21 January 2018

1 reference

Structure-based CoMFA as a predictive model - CYP2C9 inhibitors as a test case

21 January 2018

1 reference

Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

21 January 2018

1 reference

The multiple roles of computational chemistry in fragment-based drug design

21 January 2018

1 reference

Fragment-based drug discovery

21 January 2018

1 reference

Molecular docking and ligand specificity in fragment-based inhibitor discovery

21 January 2018

1 reference

Docking for fragment inhibitors of AmpC -lactamase

21 January 2018

1 reference

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide

21 January 2018

1 reference

Second-generation de novo design: a view from a medicinal chemist perspective

21 January 2018

1 reference

In silico fragment screening by replica generation (FSRG) method for fragment-based drug design

21 January 2018

1 reference

Computational fragment-based approach at PDB scale by protein local similarity

21 January 2018

1 reference

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

21 January 2018

1 reference

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

21 January 2018

1 reference

Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics

21 January 2018

1 reference

Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

21 January 2018

1 reference

Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

21 January 2018

1 reference

Constrained peptidomimetics reveal detailed geometric requirements of covalent prolyl oligopeptidase inhibitors

21 January 2018

1 reference

Covalent complexes of proteasome model with peptide aldehyde inhibitors MG132 and MG101: docking and molecular dynamics study.

21 January 2018

1 reference

Modelling beta-1,3-exoglucanase-saccharide interactions: structure of the enzyme-substrate complex and enzyme binding to the cell wall

21 January 2018

1 reference

Computational multiscale modeling in protein--ligand docking

21 January 2018

1 reference

Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4).

21 January 2018

1 reference

Reduced Catalytic Activity of P450 2A6 Mutants with Coumarin: A Computational Investigation

21 January 2018

1 reference

Polymer-drug interactions in tyrosine-derived triblock copolymer nanospheres: a computational modeling approach

21 January 2018

1 reference

Knowing when to give up: early-rejection stratagems in ligand docking

21 January 2018

1 reference

Automated docking screens: a feasibility study

21 January 2018

1 reference

VSDMIP: virtual screening data management on an integrated platform.

21 January 2018

1 reference

Data management system for distributed virtual screening

21 January 2018

1 reference

Knowledge based identification of potent antitubercular compounds using structure based virtual screening and structure interaction fingerprints

21 January 2018

1 reference

Mimicking direct protein-protein and solvent-mediated interactions in the CDP-methylerythritol kinase homodimer: a pharmacophore-directed virtual screening approach

21 January 2018

1 reference

Combining docking with pharmacophore filtering for improved virtual screening

21 January 2018

1 reference

Identification of novel serotonin 2C receptor ligands by sequential virtual screening

21 January 2018

1 reference

Development of a novel virtual screening cascade protocol to identify potential trypanothione reductase inhibitors

21 January 2018

1 reference

Scoring ligand similarity in structure-based virtual screening

21 January 2018

1 reference

Exploring novel target space: a need to partner high throughput docking and ligand-based similarity searches?

21 January 2018

1 reference

Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach.

21 January 2018

1 reference

Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening

21 January 2018

1 reference

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations

21 January 2018

1 reference

Virtual high throughput screening using combined random forest and flexible docking

21 January 2018

1 reference

Docking and chemoinformatic screens for new ligands and targets

21 January 2018

1 reference

GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function

21 January 2018

1 reference

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

21 January 2018

1 reference

Crystal structure of the human beta2 adrenergic G-protein-coupled receptor

21 January 2018

1 reference

Structure of a beta1-adrenergic G-protein-coupled receptor

21 January 2018

1 reference

The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist

21 January 2018

1 reference

Structure-based discovery of beta2-adrenergic receptor ligands

21 January 2018

1 reference

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008.

21 January 2018

1 reference

Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators

21 January 2018

1 reference

Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes

21 January 2018

1 reference

Molecular modeling of A1 and A2A adenosine receptors: comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies

21 January 2018

1 reference

Position 5.46 of the serotonin 5-HT2A receptor contributes to a species-dependent variation for the 5-HT2C agonist (R)-9-ethyl-1,3,4,10b-tetrahydro-7-trifluoromethylpyrazino[2,1-a]isoindol-6(2H)-one: impact on selectivity and toxicological evaluatio

21 January 2018

1 reference

Homology modeling and docking evaluation of aminergic G protein-coupled receptors

21 January 2018

1 reference

Identification of orthosteric and allosteric site mutations in M2 muscarinic acetylcholine receptors that contribute to ligand-selective signaling bias

21 January 2018

1 reference

Structure-based drug design: from nucleic acid to membrane protein targets

21 January 2018

1 reference

Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling

21 January 2018

1 reference

GARD: a Generally Applicable Replacement for RMSD.

21 January 2018

1 reference

Binding and enantiomeric selectivity of threonyl-tRNA synthetase.

21 January 2018

1 reference

Contact area difference (CAD): a robust measure to evaluate accuracy of protein models

21 January 2018

1 reference

Scoring confidence index: statistical evaluation of ligand binding mode predictions

21 January 2018

1 reference

A critical assessment of docking programs and scoring functions

21 January 2018

1 reference

Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode

21 January 2018

1 reference

Recognition and discrimination of DNA quadruplexes by acridine-peptide conjugates

21 January 2018

1 reference

Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression

21 January 2018

1 reference

Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences

21 January 2018

1 reference

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

21 January 2018

1 reference

Quinoline alkaloids as intercalative topoisomerase inhibitors.

21 January 2018

1 reference

Blind docking of 260 protein-ligand complexes with EADock 2.0.

21 January 2018

1 reference

Carborane clusters in computational drug design: a comparative docking evaluation using AutoDock, FlexX, Glide, and Surflex

21 January 2018

1 reference

Glycopeptide dendrimers with high affinity for the fucose-binding lectin LecB from Pseudomonas aeruginosa

21 January 2018

1 reference

Glucose-based spiro-isoxazolines: a new family of potent glycogen phosphorylase inhibitors

21 January 2018

1 reference

Comparing protein-ligand docking programs is difficult.

21 January 2018

1 reference

Docking Ligands on Protein Surfaces: The Case Study of Prion Protein

21 January 2018

1 reference

Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking

21 January 2018

1 reference

Binding of an RNA pol II Ligand to the WW Domain of Pin1 Using Molecular Dynamics Docking Simulations

21 January 2018

1 reference

Tandem Application of Virtual Screening and NMR Experiments in the Discovery of Brand New DNA Quadruplex Groove Binders

21 January 2018

1 reference

Use of an induced fit receptor structure in virtual screening

21 January 2018

23

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Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking

25 November 2024

45

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Effect of input differences on the results of docking calculations

25 November 2024

51

1 reference

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

25 November 2024

60

1 reference

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

25 November 2024

68

1 reference

New method for fast and accurate binding-site identification and analysis

25 November 2024

82

1 reference

Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps

25 November 2024

100

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Scoring function for DNA-drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories

25 November 2024

123

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Better than random? The chemotype enrichment problem

25 November 2024

127

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Docking and Virtual Screening Using Distributed Grid Technology

25 November 2024

133

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Novel method for generating structure-based pharmacophores using energetic analysis

25 November 2024

135

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Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions

25 November 2024

164

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Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures

25 November 2024

165

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Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations

25 November 2024

167

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Docking to heme proteins.

25 November 2024

178

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25 November 2024

Identifiers

DOI

10.1002/JMR.1077

1 reference

24 August 2017

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