Docking validation resources: protein family and ligand flexibility experiments

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Docking validation resources: protein family and ligand flexibility experiments is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/jcisd/MukherjeeBR10
P356DOI10.1021/CI1001982
P932PMC publication ID3058392
P698PubMed publication ID21033739
P5875ResearchGate publication ID47632479

P2093author name stringSudipto Mukherjee
Robert C Rizzo
Trent E Balius
P2860cites workThe Protein Data BankQ24515306
DOCK 6: combining techniques to model RNA-small molecule complexesQ24657524
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinitiesQ24675698
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databasesQ27231136
Structure of native and apo carbonic anhydrase II and structure of some of its anion-ligand complexesQ27642161
UCSF Chimera--a visualization system for exploratory research and analysisQ27860666
The Amber biomolecular simulation programsQ27860745
Gaussian docking functionsQ28208578
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracyQ28251042
Automated docking screens: a feasibility studyQ28256939
Community benchmarks for virtual screeningQ28268675
Automated docking of flexible ligands: applications of AutoDockQ28285420
Recommendations for evaluation of computational methodsQ28755020
Development and testing of a general amber force fieldQ29547642
Rational design of potent sialidase-based inhibitors of influenza virus replicationQ29616647
Improved protein-ligand docking using GOLDQ29616787
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screeningQ29617343
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validationQ29617869
Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase.Q30333072
Novel procedure for modeling ligand/receptor induced fit effects.Q30352584
The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.Q30356303
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.Q30370020
Ligand-protein database: linking protein-ligand complex structures to binding dataQ30662705
Evaluation of the FLEXX incremental construction algorithm for protein-ligand dockingQ30822076
Virtual screening of chemical librariesQ33209939
Virtual ligand screening: strategies, perspectives and limitationsQ33247681
A geometric approach to macromolecule-ligand interactionsQ34280176
The many roles of computation in drug discoveryQ34307063
Flexibases: a way to enhance the use of molecular docking methodsQ34319987
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structuresQ34323005
The PDBbind database: methodologies and updatesQ34424778
Development and validation of a modular, extensible docking program: DOCK 5.Q34588100
Structure-based strategies for drug design and discoveryQ35748974
An improved relaxed complex scheme for receptor flexibility in computer-aided drug designQ36838120
Soft docking and multiple receptor conformations in virtual screeningQ41968000
Bias, reporting, and sharing: computational evaluations of docking methodsQ42639520
Protein flexibility in ligand docking and virtual screening to protein kinases.Q44786754
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.Q46036230
Molecular docking to ensembles of protein structuresQ46668232
Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomersQ47625159
Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations.Q51869959
A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors.Q51932664
Diverse, high-quality test set for the validation of protein-ligand docking performance.Q55043208
Binding MOAD (Mother Of All Databases)Q81878003
P433issue11
P921main subjectprotein familyQ417841
P304page(s)1986-2000
P577publication date2010-10-29
P1433published inJournal of Chemical Information and ModelingQ3007982
P1476titleDocking validation resources: protein family and ligand flexibility experiments
P478volume50

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