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Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

https://doi.org/10.1021/jm800071v
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1 of the 43 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-11): 10.1126/science.291.5501.134 (notice 2002-12-20).

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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199902)20:3<287::aid-jcc1>3.0.co;2-hopenalex-snapshot
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19981115)33:3<417::aid-prot10>3.0.co;2-8openalex-snapshot
Analysis of domain motions by approximate normal mode calculations
inferredcites →https://doi.org/10.1002/jcc.20035openalex-snapshot
Development and testing of a general amber force field
inferredcites →https://doi.org/10.1002/jcc.540150503openalex-snapshot
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
inferredcites →https://doi.org/10.1002/pro.5560060807openalex-snapshot
Bayesian statistical analysis of protein side‐chain rotamer preferences
inferredcites →https://doi.org/10.1002/pro.5560070411openalex-snapshot
Flexible ligand docking using conformational ensembles
inferredcites →https://doi.org/10.1002/prot.10637openalex-snapshot
Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot
Protein–ligand docking: Current status and future challenges
inferredcites →https://doi.org/10.1002/prot.21579openalex-snapshot
Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21735openalex-snapshot
Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility
inferredcites →https://doi.org/10.1002/prot.340080302openalex-snapshot
Automated docking of substrates to proteins by simulated annealing
inferredcites →https://doi.org/10.1002/prot.340140216openalex-snapshot
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
inferredcites →https://doi.org/10.1002/prot.340170408openalex-snapshot
Essential dynamics of proteins
inferredcites →https://doi.org/10.1002/prot.340220408openalex-snapshot
Multiple modes of ligand recognition: Crystal structures of cyclin‐dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine
inferredcites →https://doi.org/10.1006/jmbi.1993.1170openalex-snapshot
Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction
inferredcites →https://doi.org/10.1006/jmbi.1994.1052openalex-snapshot
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot
FlexE: efficient molecular docking considering protein structure variations
inferredcites →https://doi.org/10.1007/bf01589116openalex-snapshot
On the limited memory BFGS method for large scale optimization
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/j.bbapap.2005.07.045openalex-snapshot
Accounting for global protein deformability during protein–protein and protein–ligand docking
inferredcites →https://doi.org/10.1016/j.jmgm.2005.12.005openalex-snapshot
Automatic atom type and bond type perception in molecular mechanical calculations
inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot
Ligand docking to proteins with discrete side-chain flexibility
inferredcites →https://doi.org/10.1016/s0969-2126(01)00598-6openalex-snapshot
Inhibitor Binding to Active and Inactive CDK2
inferredcites →https://doi.org/10.1016/s1359-0278(97)00024-2openalex-snapshot
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
inferredcites →https://doi.org/10.1016/s1367-5931(00)00217-9openalex-snapshot
High-throughput docking for lead generation
inferredcites →https://doi.org/10.1021/j100142a004openalex-snapshot
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
inferredcites →https://doi.org/10.1021/jm010117dopenalex-snapshot
Oxindole-Based Inhibitors of Cyclin-Dependent Kinase 2 (CDK2): Design, Synthesis, Enzymatic Activities, and X-ray Crystallographic Analysis
inferredcites →https://doi.org/10.1021/jm990628oopenalex-snapshot
Identification of Novel Purine and Pyrimidine Cyclin-Dependent Kinase Inhibitors with Distinct Molecular Interactions and Tumor Cell Growth Inhibition Profiles
inferredcites →https://doi.org/10.1021/jp991997zopenalex-snapshot
Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design
inferredcites →https://doi.org/10.1021/jp993073hopenalex-snapshot
Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1038/nsb842openalex-snapshot
Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor
inferredcites →https://doi.org/10.1063/1.466707openalex-snapshot
Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration
inferredcites →https://doi.org/10.1073/pnas.0507603102openalex-snapshot
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
inferredcites →https://doi.org/10.1074/jbc.m102034200openalex-snapshot
The Cyclin-dependent Kinases cdk2 and cdk5 Act by a Random, Anticooperative Kinetic Mechanism
inferredcites →https://doi.org/10.1093/bioinformatics/bti825openalex-snapshot
Multiple Alignment of protein structures and sequences for VMD
inferredcites →https://doi.org/10.1093/protein/14.1.1openalex-snapshot
Conformational change of proteins arising from normal mode calculations
inferredcites →https://doi.org/10.1103/physrevlett.77.1905openalex-snapshot
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
inferredcites →https://doi.org/10.1126/science.291.5501.134openalex-snapshot
Prevention of Chemotherapy-Induced Alopecia in Rats by CDK Inhibitors
inferredcites →https://doi.org/10.1146/annurev.pharmtox.43.100901.140216openalex-snapshot
Protein Flexibility and Computer-Aided Drug Design

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/0471266949.bmc148openalex-snapshot
Protein Flexibility in In Silico Screening
inferred← citeshttps://doi.org/10.1002/9781118681121.ch6openalex-snapshot
Allostery as Structure‐Encoded Collective Dynamics
inferred← citeshttps://doi.org/10.1002/9783527633326.ch15openalex-snapshot
Target‐Based Virtual Screening on Small‐Molecule Protein Binding Sites
inferred← citeshttps://doi.org/10.1002/9783527633326.ch6openalex-snapshot
Docking Methods for Virtual Screening: Principles and Recent Advances
inferred← citeshttps://doi.org/10.1002/9783527633326.ch8openalex-snapshot
Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms
inferred← citeshttps://doi.org/10.1002/cmdc.200800301openalex-snapshot
Virtual Screening and Biological Characterization of Novel Histone Arginine Methyltransferase PRMT1 Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.201500086openalex-snapshot
Protein Flexibility in Drug Discovery: From Theory to Computation
inferred← citeshttps://doi.org/10.1002/jcc.21923openalex-snapshot
Efficient inclusion of receptor flexibility in grid‐based protein–ligand docking*
inferred← citeshttps://doi.org/10.1002/jcc.23087openalex-snapshot
Modeling loop backbone flexibility in receptor‐ligand docking simulations
inferred← citeshttps://doi.org/10.1002/minf.200900078openalex-snapshot
In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding
inferred← citeshttps://doi.org/10.1002/pro.366openalex-snapshot
A flexible docking scheme to explore the binding selectivity of PDZ domains
inferred← citeshttps://doi.org/10.1002/pro.3732openalex-snapshot
Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
inferred← citeshttps://doi.org/10.1002/pro.711openalex-snapshot
Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
inferred← citeshttps://doi.org/10.1002/prot.22841openalex-snapshot
Large‐scale comparison of protein essential dynamics from molecular dynamics simulations and coarse‐grained normal mode analyses
inferred← citeshttps://doi.org/10.1002/prot.23225openalex-snapshot
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
inferred← citeshttps://doi.org/10.1002/prot.23239openalex-snapshot
H‐bond network optimization in protein–protein complexes: Are all‐atom force field scores enough?
inferred← citeshttps://doi.org/10.1002/prot.24021openalex-snapshot
Exploring c‐Met kinase flexibility by sampling and clustering its conformational space
inferred← citeshttps://doi.org/10.1002/prot.26027openalex-snapshot
Predicting cryptic ligand binding sites based on normal modes guided conformational sampling
inferred← citeshttps://doi.org/10.1002/qua.25678openalex-snapshot
Computational chemistry in drug lead discovery and design
inferred← citeshttps://doi.org/10.1002/wcms.29openalex-snapshot
Receptor flexibility in small‐molecule docking calculations
inferred← citeshttps://doi.org/10.1007/7653_2015_56openalex-snapshot
Incorporating Receptor Flexibility into Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-1-4939-2914-6_18openalex-snapshot
The Dynamic Process of Drug–GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics
inferred← citeshttps://doi.org/10.1007/978-1-4939-6798-8_5openalex-snapshot
Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-61779-465-0_11openalex-snapshot
Normal Mode-Based Approaches in Receptor Ensemble Docking
inferred← citeshttps://doi.org/10.1007/978-3-319-02970-2_11openalex-snapshot
Exploiting Protein Intrinsic Flexibility in Drug Design
inferred← citeshttps://doi.org/10.1007/978-3-319-09976-7_11openalex-snapshot
Protein Ligand Docking in Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-94-017-9257-8_15openalex-snapshot
(How to) Profit from Molecular Dynamics-based Ensemble Docking
inferred← citeshttps://doi.org/10.1007/s00249-010-0592-0openalex-snapshot
How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
inferred← citeshttps://doi.org/10.1007/s10822-010-9356-2openalex-snapshot
Chemical space sampling by different scoring functions and crystal structures
inferred← citeshttps://doi.org/10.1007/s10822-011-9415-3openalex-snapshot
Molecular motions in drug design: the coming age of the metadynamics method
inferred← citeshttps://doi.org/10.1007/s10822-011-9523-0openalex-snapshot
Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge
inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.006openalex-snapshot
No dance, no partner! A tale of receptor flexibility in docking and virtual screening
inferred← citeshttps://doi.org/10.1016/j.abb.2015.08.002openalex-snapshot
Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
inferred← citeshttps://doi.org/10.1016/j.bbadis.2024.167261openalex-snapshot
PURA and GLUT1: Sweet partners for brain health
inferred← citeshttps://doi.org/10.1016/j.bmc.2011.06.022openalex-snapshot
Discovery of benzimidazole derivatives as novel multi-target EGFR, VEGFR-2 and PDGFR kinase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bpj.2011.11.4008openalex-snapshot
Discrete Molecular Dynamics Distinguishes Nativelike Binding Poses from Decoys in Difficult Targets
inferred← citeshttps://doi.org/10.1016/j.coph.2010.09.001openalex-snapshot
Computer-aided drug-discovery techniques that account for receptor flexibility
inferred← citeshttps://doi.org/10.1016/j.jmgm.2009.08.012openalex-snapshot
Induced-fit docking studies of the active and inactive states of protein tyrosine kinases
inferred← citeshttps://doi.org/10.1017/s0033583512000066openalex-snapshot
Protein flexibility in docking and surface mapping
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c01243openalex-snapshot
Computation of the Protein Conformational Transition Pathway on Ligand Binding by Linear Response-Driven Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b01110openalex-snapshot
Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b01022openalex-snapshot
Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations
inferred← citeshttps://doi.org/10.1021/acsomega.0c00522openalex-snapshot
Protein Binding Pocket Optimization for Virtual High-Throughput Screening (vHTS) Drug Discovery
inferred← citeshttps://doi.org/10.1021/bi2004558openalex-snapshot
Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
inferred← citeshttps://doi.org/10.1021/ci100076jopenalex-snapshot
Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation
inferred← citeshttps://doi.org/10.1021/ci100218topenalex-snapshot
Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands
inferred← citeshttps://doi.org/10.1021/ci100461kopenalex-snapshot
A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins
inferred← citeshttps://doi.org/10.1021/ci2004847openalex-snapshot
On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking
inferred← citeshttps://doi.org/10.1021/ci300478yopenalex-snapshot
Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark
inferred← citeshttps://doi.org/10.1021/ci500299hopenalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy
inferred← citeshttps://doi.org/10.1021/ci8003732openalex-snapshot
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
inferred← citeshttps://doi.org/10.1021/ci8004034openalex-snapshot
Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations
inferred← citeshttps://doi.org/10.1021/cr900095eopenalex-snapshot
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
inferred← citeshttps://doi.org/10.1021/ct300117jopenalex-snapshot
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
inferred← citeshttps://doi.org/10.1021/jm200979xopenalex-snapshot
Identification of Binding Specificity-Determining Features in Protein Families
inferred← citeshttps://doi.org/10.1021/jp108286ropenalex-snapshot
VX680 Binding in Aurora A: π−π Interactions Involving the Conserved Aromatic Amino Acid of the Flexible Glycine-Rich Loop
inferred← citeshttps://doi.org/10.1039/9781849735377-00223openalex-snapshot
Accounting for Target Flexibility During Ligand–Receptor Docking
inferred← citeshttps://doi.org/10.1039/c6ra12084aopenalex-snapshot
Computational study of the binding orientation and affinity of PPARγ agonists: inclusion of ligand-induced fit by cross-docking
inferred← citeshttps://doi.org/10.1073/pnas.0904214106openalex-snapshot
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
inferred← citeshttps://doi.org/10.1085/jgp.200910368openalex-snapshot
On the functional significance of soft modes predicted by coarse-grained models for membrane proteins
inferred← citeshttps://doi.org/10.1111/cbdd.13764openalex-snapshot
GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking
inferred← citeshttps://doi.org/10.1142/9789814335058_0020openalex-snapshot
COMPUTATIONAL GENERATION INHIBITOR-BOUND CONFORMERS OF P38 MAP KINASE AND COMPARISON WITH EXPERIMENTS
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002068openalex-snapshot
Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002154openalex-snapshot
Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004586openalex-snapshot
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006705openalex-snapshot
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures
inferred← citeshttps://doi.org/10.1371/journal.pone.0158063openalex-snapshot
Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins
inferred← citeshttps://doi.org/10.1517/17460441.2015.1078308openalex-snapshot
Flexible receptor docking for drug discovery
inferred← citeshttps://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferred← citeshttps://doi.org/10.1517/17460441003713462openalex-snapshot
Tackling the challenges posed by target flexibility in drug design
inferred← citeshttps://doi.org/10.2174/156802611794863544openalex-snapshot
Accounting for Induced-Fit Effects in Docking: What is Possible and What is Not?
inferred← citeshttps://doi.org/10.2174/978160805142711101010099openalex-snapshot
Receptor Flexibility in Ligand Docking and Virtual Screening
inferred← citeshttps://doi.org/10.3389/fmicb.2015.00660openalex-snapshot
Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/ijms11103623openalex-snapshot
SwarmDock and the Use of Normal Modes in Protein-Protein Docking
inferred← citeshttps://doi.org/10.3390/ijms12021316openalex-snapshot
Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
inferred← citeshttps://doi.org/10.34133/csbj.0008openalex-snapshot
Antibacterial Drug Discovery: Deep Learning Successes and Challenges through the Structural Biology Lens
inferred← citeshttps://doi.org/10.4155/fmc.15.150openalex-snapshot
Sampling of Conformational Ensemble for Virtual Screening Using Molecular Dynamics Simulations and Normal Mode Analysis
inferred← citeshttps://doi.org/10.6092/unibo/amsdottorato/6330openalex-snapshot
Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening
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