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

scientific article published on March 2009

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/jcisd/RuedaBA09
P356DOI10.1021/CI8003732
P932PMC publication ID2891173
P698PubMed publication ID19434904
P5875ResearchGate publication ID24420350

P50authorRuben AbagyanQ44682954
P2093author name stringManuel Rueda
Giovanni Bottegoni
P2860cites workThe Protein Data BankQ24515306
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structuresQ24545785
Flexible ligand docking to multiple receptor conformations: a practical alternativeQ24650066
A consensus view of protein dynamicsQ24682188
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solutionQ27650851
Molecular dynamics and protein functionQ28248486
Docking essential dynamics eigenstructuresQ28258497
Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid stateQ28295069
A hierarchy of timescales in protein dynamics is linked to enzyme catalysisQ29616405
Essential dynamics of proteinsQ29616843
Pocketome via comprehensive identification and classification of ligand binding envelopes.Q30350345
Protein structures in virtual screening: a case study with CDK2.Q30352402
Novel procedure for modeling ligand/receptor induced fit effects.Q30352584
Normal modes and essential dynamics.Q51887481
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.Q51933455
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy.Q52878047
Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase.Q53746377
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic AnalysisQ56688821
Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential DynamicsQ57975961
Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitorsQ58571868
Locating the active sites of enzymes using mechanical propertiesQ61836416
Normal mode analysis of G-actinQ70602553
Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysisQ70980716
Flexibility analysis of enzyme active sites by crystallographic temperature factorsQ73218028
Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening resultsQ80697151
Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test caseQ80850175
Exploring the Essential Dynamics of B-DNAQ86864345
Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.Q30357936
Exploring experimental sources of multiple protein conformations in structure-based drug design.Q30362194
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.Q30370020
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteinsQ30421728
Electrostatic funneling of substrate in mitochondrial inner membrane carriersQ30482734
Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor familyQ31093553
The role of dynamics in enzyme activityQ33185384
Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3beta inhibitorsQ33228824
Accommodating protein flexibility in computational drug designQ33825095
Protein dynamics from NMR.Q34019517
Normal modes as refinement parameters for the F-actin modelQ34128277
Conformational changes observed in enzyme crystal structures upon substrate bindingQ34386848
Flexible docking in solution using metadynamicsQ34396573
Implications of protein flexibility for drug discoveryQ35167908
Conformational flexibility models for the receptor in structure based drug design.Q35181130
Dynamics of different functional parts of bacteriorhodopsin: H-2H labeling and neutron scatteringQ36061363
Protein-ligand docking: current status and future challengesQ36544700
Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?Q36638823
An improved relaxed complex scheme for receptor flexibility in computer-aided drug designQ36838120
Overcoming the inadequacies or limitations of experimental structures as drug targets by using computational modeling tools and molecular dynamics simulationsQ36931811
Target flexibility: an emerging consideration in drug discovery and designQ37240137
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitorQ37549050
Dynamics of a small globular protein in terms of low-frequency vibrational modesQ37615047
Molecular dynamics of biological macromolecules: a brief history and perspectiveQ40603907
The effect of multiple binding modes on empirical modeling of ligand docking to proteinsQ41666696
Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysisQ42844242
Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug designQ43081937
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).Q43181588
Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.Q44784463
Protein flexibility in ligand docking and virtual screening to protein kinases.Q44786754
Predictions of protein flexibility: first-order measuresQ46120384
Representing receptor flexibility in ligand docking through relevant normal modes.Q46211444
Unveiling the full potential of flexible receptor docking using multiple crystallographic structuresQ46563192
Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysisQ46802286
Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulationsQ47430898
Analysis of catalytic residues in enzyme active sitesQ47614986
Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross dockingQ47669698
Fully automated molecular mechanics based induced fit protein-ligand docking method.Q51868440
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)716-725
P577publication date2009-03-01
P1433published inJournal of Chemical Information and ModelingQ3007982
P1476titleConsistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes
P478volume49

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cites work (P2860)
Q40496890A flexible docking scheme to explore the binding selectivity of PDZ domains
Q34402706ALiBERO: evolving a team of complementary pocket conformations rather than a single leader
Q51088846Applications of Normal Mode Analysis Methods in Computational Protein Design.
Q28484330Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening?
Q37848281Challenges and advances in computational docking: 2009 in review
Q30423071Compound activity prediction using models of binding pockets or ligand properties in 3D.
Q34440071Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors
Q35630615Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures
Q34120783Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets
Q39096521Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping
Q24633124Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
Q90353407Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain
Q41488333ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability
Q51532081Efficient inclusion of receptor flexibility in grid-based protein-ligand docking.
Q30437388GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex
Q44622243Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering
Q56984187How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
Q30391029In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding
Q28536904In silico mechanistic profiling to probe small molecule binding to sulfotransferases
Q28552181Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins
Q44789723Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach.
Q51334109Modeling loop backbone flexibility in receptor-ligand docking simulations.
Q38307338Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target.
Q37843834Molecular motions in drug design: the coming age of the metadynamics method
Q36502439Pocket-based drug design: exploring pocket space
Q30405812Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
Q38428430Protein Flexibility in Drug Discovery: From Theory to Computation
Q57990955Protein Ligand DockingDocking in Drug DiscoveryDrug Discovery
Q26864013Protein flexibility in docking and surface mapping
Q33659311Rapid flexible docking using a stochastic rotamer library of ligands
Q33893113Recent trends and observations in the design of high-quality screening collections
Q38783140Receptor-ligand molecular docking
Q42081112Recipes for the selection of experimental protein conformations for virtual screening
Q35369246SEABED: Small molEcule activity scanner weB servicE baseD.
Q38939477Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis
Q27022502Structure-based virtual screening for drug discovery: a problem-centric review
Q34408300Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification
Q41239235SwarmDock and the use of normal modes in protein-protein docking
Q28478200Systematic exploitation of multiple receptor conformations for virtual ligand screening
Q30419540Tackling the challenges posed by target flexibility in drug design
Q30382761Template-based protein modeling: recent methodological advances.
Q47234473The Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review
Q39977512The anisotropic network model web server at 2015 (ANM 2.0).
Q38594557Understanding the challenges of protein flexibility in drug design.

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