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On the use of distance constraints in protein–protein docking computations
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Outgoing claims: the papers this work cites, builds on, or argues with.
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New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen A?-like peptide bound to thrombin(S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program
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A novel shape complementarity scoring function for protein‐protein docking
inferredcites →https://doi.org/10.1002/prot.10383openalex-snapshot
ICM‐DISCO docking by global energy optimization with fully flexible side‐chains
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Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
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Protein–protein docking benchmark 2.0: An update
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ZRANK: Reranking protein docking predictions with an optimized energy function
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Annexin A2/P11 interaction: New insights into annexin A2 tetramer structure by chemical crosslinking, high‐resolution mass spectrometry, and computational modeling
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Integrating statistical pair potentials into protein complex prediction
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Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.21920openalex-snapshot
A combination of rescoring and refinement significantly improves protein docking performance
inferredcites →https://doi.org/10.1002/prot.22564openalex-snapshot
Present and future challenges and limitations in protein–protein docking
inferredcites →https://doi.org/10.1002/prot.22764openalex-snapshot
Performance of ZDOCK and ZRANK in CAPRI rounds 13–19
inferredcites →https://doi.org/10.1002/prot.22772openalex-snapshot
Selection of near‐native poses in CAPRI rounds 13‐19
inferredcites →https://doi.org/10.1002/prot.22790openalex-snapshot
An integrated suite of fast docking algorithms
inferredcites →https://doi.org/10.1002/prot.22793openalex-snapshot
CAPRI targets T29–T42: Proving ground for new docking procedures
inferredcites →https://doi.org/10.1002/prot.22797openalex-snapshot
MDockPP: A hierarchical approach for protein‐protein docking and its application to CAPRI rounds 15–19
inferredcites →https://doi.org/10.1002/prot.22808openalex-snapshot
Binding site prediction and improved scoring during flexible protein–protein docking with ATTRACT
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Docking and scoring protein interactions: CAPRI 2009
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Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19
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Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
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Rapid refinement of protein interfaces incorporating solvation: application to the docking problem
inferredcites →https://doi.org/10.1006/jmbi.1999.2820openalex-snapshot
Model of the Ran-RCC1 Interaction using Biochemical and Docking Experiments
inferredcites →https://doi.org/10.1007/s00018-007-7451-xopenalex-snapshot
The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
inferredcites →https://doi.org/10.1007/s10858-006-9065-2openalex-snapshot
A simple and reliable approach to docking protein–protein complexes from very sparse NOE-derived intermolecular distance restraints
inferredcites →https://doi.org/10.1007/s10898-008-9293-yopenalex-snapshot
A reassessment of the Snyman–Fatti dynamic search trajectory method for unconstrained global optimization
inferredcites →https://doi.org/10.1016/0022-2836(71)90324-xopenalex-snapshot
The interpretation of protein structures: Estimation of static accessibility
inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot
High-resolution protein–protein docking
inferredcites →https://doi.org/10.1016/j.sbi.2010.02.001openalex-snapshot
Accounting for conformational changes during protein–protein docking
inferredcites →https://doi.org/10.1016/s0076-6879(07)23004-6openalex-snapshot
Rigid Body Refinement of Protein Complexes with Long‐Range Distance Restraints from Pulsed Dipolar ESR
inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1016/s1090-7807(02)00014-9openalex-snapshot
The Xplor-NIH NMR molecular structure determination package
inferredcites →https://doi.org/10.1017/cbo9780511608797openalex-snapshot
A Treatise on the Analytical Dynamics of Particles and Rigid Bodies
inferredcites →https://doi.org/10.1021/ac0487294openalex-snapshot
Chemical Cross-Linking and High-Performance Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Protein Interaction Analysis: Application to a Calmodulin/Target Peptide Complex
inferredcites →https://doi.org/10.1021/bi036149fopenalex-snapshot
Mapping the Topology and Determination of a Low-Resolution Three-Dimensional Structure of the Calmodulin−Melittin Complex by Chemical Cross-Linking and High-Resolution FTICRMS: Direct Demonstration of Multiple Binding Modes
inferredcites →https://doi.org/10.1021/bi060874jopenalex-snapshot
Position of Synaptotagmin I at the Membrane Interface: Cooperative Interactions of Tandem C2 Domains
inferredcites →https://doi.org/10.1021/bi800734wopenalex-snapshot
Use of Multidimensional Fluorescence Resonance Energy Transfer To Establish the Orientation of Cholecystokinin Docked at the Type A Cholecystokinin Receptor
inferredcites →https://doi.org/10.1021/bi900300ropenalex-snapshot
Structural Insights into the Calmodulin−Munc13 Interaction Obtained by Cross-Linking and Mass Spectrometry
inferredcites →https://doi.org/10.1021/bi9004705openalex-snapshot
Elucidation of the Molecular Basis of Cholecystokinin Peptide Docking to Its Receptor Using Site-Specific Intrinsic Photoaffinity Labeling and Molecular Modeling
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1021/ja028893dopenalex-snapshot
Docking of Protein−Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1 H N / 15 N Chemical Shift Mapping and Backbone 15 N− 1 H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics
inferredcites →https://doi.org/10.1021/pr060154zopenalex-snapshot
Protein Cross-Linking Analysis Using Mass Spectrometry, Isotope-Coded Cross-Linkers, and Integrated Computational Data Processing
inferredcites →https://doi.org/10.1038/embor.2008.179openalex-snapshot
Structural insights into microneme protein assembly reveal a new mode of EGF domain recognition
inferredcites →https://doi.org/10.1038/nprot.2007.406openalex-snapshot
Version 1.2 of the Crystallography and NMR system
inferredcites →https://doi.org/10.1039/c005060copenalex-snapshot
Protein–protein docking tested in blind predictions: the CAPRI experiment
inferredcites →https://doi.org/10.1073/pnas.0407456101openalex-snapshot
Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry
inferredcites →https://doi.org/10.1073/pnas.0900693106openalex-snapshot
The assembled structure of a complete tripartite bacterial multidrug efflux pump
inferredcites →https://doi.org/10.1073/pnas.2232255100openalex-snapshot
Identification of the protein kinase A regulatory R I α-catalytic subunit interface by amide H/ 2 H exchange and protein docking
inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
inferredcites →https://doi.org/10.1073/pnas.97.16.9021openalex-snapshot
Accurate and rapid docking of protein–protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization
inferredcites →https://doi.org/10.1074/jbc.m208956200openalex-snapshot
Mapping the Heparin-binding Site on the13–14F3 Fragment of Fibronectin
inferredcites →https://doi.org/10.1074/jbc.m700970200openalex-snapshot
Conformational Fluctuations Coupled to the Thiol-Disulfide Transfer between Thioredoxin and Arsenate Reductase in Bacillus subtilis
inferredcites →https://doi.org/10.1074/mcp.r000001-mcp201openalex-snapshot
Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics
inferredcites →https://doi.org/10.1074/mcp.r110.000067openalex-snapshot
Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data
inferredcites →https://doi.org/10.1093/bioinformatics/btn093openalex-snapshot
3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
inferredcites →https://doi.org/10.1093/bioinformatics/btn334openalex-snapshot
Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions
inferredcites →https://doi.org/10.1093/bioinformatics/btq582openalex-snapshot
FILTREST3D: discrimination of structural models using restraints from experimental data
inferredcites →https://doi.org/10.1093/nar/gkh354openalex-snapshot
ClusPro: a fully automated algorithm for protein-protein docking
inferredcites →https://doi.org/10.1093/protein/4.2.177openalex-snapshot
Distance-constrained molecular docking by simulated annealing
inferredcites →https://doi.org/10.1110/ps.04941505openalex-snapshot
Physicochemical and residue conservation calculations to improve the ranking of protein–protein docking solutions
inferredcites →https://doi.org/10.1110/ps.51201openalex-snapshot
Quantitative evaluation of the lengths of homobifunctional protein cross‐linking reagents used as molecular rulers
inferredcites →https://doi.org/10.1111/j.1742-4658.2004.04473.xopenalex-snapshot
Data‐driven docking for the study of biomolecular complexes
inferredcites →https://doi.org/10.1146/annurev.biochem.77.060407.135530openalex-snapshot
Integrating Diverse Data for Structure Determination of Macromolecular Assemblies
inferredcites →https://doi.org/10.1371/journal.pone.0017695openalex-snapshot
CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
inferredcites →https://doi.org/10.1529/biophysj.104.050187openalex-snapshot
Distance-Restrained Docking of Rifampicin and Rifamycin SV to RNA Polymerase Using Systematic FRET Measurements: Developing Benchmarks of Model Quality and Reliability
inferredcites →https://doi.org/10.2174/138920308783565741openalex-snapshot
Recent Progress and Future Directions in Protein-Protein Docking
inferredcites →https://doi.org/10.2210/pdb2jzb/pdbopenalex-snapshot
Solution structure of the complex between E.coli NusA-AR2 and RNAP-aCTD
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Computational Modeling of Designed Ankyrin Repeat Protein Complexes with Their Targets
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Using chemical shift perturbation to characterise ligand binding
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Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
inferred← citeshttps://doi.org/10.1021/jacs.7b11056openalex-snapshot
A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron–Electron Resonance Spectroscopy
inferred← citeshttps://doi.org/10.1074/mcp.m112.020198openalex-snapshot
A Critical Assessment of Information-guided Protein–Protein Docking Predictions
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts182openalex-snapshot
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
inferred← citeshttps://doi.org/10.1186/s12900-015-0050-4openalex-snapshot
Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures
inferred← citeshttps://doi.org/10.1371/journal.pone.0073411openalex-snapshot
Cross-Link Guided Molecular Modeling with ROSETTA
inferred← citeshttps://doi.org/10.1515/bams-2014-0013openalex-snapshot
Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction
inferred← citeshttps://doi.org/10.1613/jair.4193openalex-snapshot
A Constraint Solver for Flexible Protein Model
inferred← citeshttps://doi.org/10.3390/biology4020282openalex-snapshot
NPPD: A Protein-Protein Docking Scoring Function Based on Dyadic Differences in Networks of Hydrophobic and Hydrophilic Amino Acid Residues
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