Data‐driven docking for the study of biomolecular complexes

No abstract is available for this paper.

• Publication year

  2005

• Venue

  The FEBS Journal

• Publication date

  2005-01-01

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1111/j.1742-4658.2004.04473.xPMID 15654870
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein.

  2004cited by this paper
• ProMate: a structure based prediction program to identify the location of protein-protein binding sites.

  2004cited by this paper
• Structure-Based Assembly of Protein Complexes in Yeast

  2004cited by this paper
• Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements

  2004cited by this paper
• Coupling of Folding and Binding of Thymosin β4 upon Interaction with Monomeric Actin Monitored by Nuclear Magnetic Resonance*

  2004cited by this paper
• Predictions of protein flexibility: First‐order measures

  2004cited by this paper
• Synchrotron radiolysis and mass spectrometry: a new approach to research on the actin cytoskeleton.

  2004cited by this paper
• SOS-NMR: a saturation transfer NMR-based method for determining the structures of protein-ligand complexes.

  2004cited by this paper
• A combinatorial selective labeling method for the assignment of backbone amide NMR resonances.

  2004cited by this paper
• Hydrogen/Deuterium Exchange Mass Spectrometry for Investigating Protein-Ligand Interactions

  2004cited by this paper
• Dimerization of the Transmembrane Domain of Integrin αIIb Subunit in Cell Membranes*

  2004cited by this paper
• Structure of a flavivirus envelope glycoprotein in its low‐pH‐induced membrane fusion conformation

  2004cited by this paper
• Protein-protein docking: is the glass half-full or half-empty?

  2004cited by this paper
• Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.

  2004cited by this paper
• Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP

  2004cited by this paper
• Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes

  2004cited by this paper
• A structural perspective on protein-protein interactions.

  2004cited by this paper
• Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein-DNA interactions.

  2004cited by this paper
• High-sensitivity mass spectrometry for imaging subunit interactions: hydrogen/deuterium exchange.

  2004cited by this paper
• A docking approach to the study of copper trafficking proteins; interaction between metallochaperones and soluble domains of copper ATPases.

  2004cited by this paper
• A structural model of EmrE, a multi-drug transporter from Escherichia coli.

  2004cited by this paper
• NMR Solution Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase in Complex with a Paxillin LD Peptide

  2004cited by this paper
• Improving the Accuracy of NMR Structures of Large Proteins Using Pseudocontact Shifts as Long-Range Restraints

  2004cited by this paper
• Computational simulations of interactions of scorpion toxins with the voltage-gated potassium ion channel.

  2004cited by this paper
• Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.

  2004cited by this paper
• Structural Basis for the Co-activation of Protein Kinase B by T-cell Leukemia-1 (TCL1) Family Proto-oncoproteins*

  2004cited by this paper
• A Classic Zinc Finger from Friend of GATA Mediates an Interaction with the Coiled-coil of Transforming Acidic Coiled-coil 3*

  2004cited by this paper
• Preferential Substrate Binding Orientation by the Molecular Chaperone HscA*

  2004cited by this paper
• Insight into molecular interactions between two PB1 domains.

  2004cited by this paper
• Model for the yeast cofactor A-beta-tubulin complex based on computational docking and mutagensis.

  2004cited by this paper
• Optimal bundling of transmembrane helices using sparse distance constraints

  2004cited by this paper
• Multivalent Mechanism of Membrane Insertion by the FYVE Domain*

  2004cited by this paper
• Evolutionary epitopes of Hsp90 and p23: implications for their interaction

  2004cited by this paper
• Biophysical characterization of the complex between double-stranded RNA and the N-terminal domain of the NS1 protein from influenza A virus: evidence for a novel RNA-binding mode.

  2004cited by this paper
• Experimentally biased model structure of the Hsc70/auxilin complex: Substrate transfer and interdomain structural change

  2004cited by this paper
• PathBLAST: a tool for alignment of protein interaction networks

  2004cited by this paper
• Physical Interaction between Replication Protein A and Rad51 Promotes Exchange on Single-stranded DNA*

  2004cited by this paper
• Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97

  2004cited by this paper
• Guided docking approaches to structure-based design and screening.

  2004cited by this paper
• Biological role and structural mechanism of twinfilin–capping protein interaction

  2004cited by this paper
• Empirical force fields for biological macromolecules: Overview and issues

  2004cited by this paper
• Specificity of the Interaction between Ubiquitin-associated Domains and Ubiquitin*

  2004cited by this paper
• 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.

  2004cited by this paper
• Structure and DNA‐binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis

  2004cited by this paper
• Convergent recognition of the IgE binding site on the high-affinity IgE receptor.

  2004cited by this paper
• The dimeric and trimeric solution structures of the multidomain complement protein properdin by X-ray scattering, analytical ultracentrifugation and constrained modelling.

  2004cited by this paper
• Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling*

  2004cited by this paper
• Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE

  2004cited by this paper
• Protein-Nucleic Acid Interactions and the Expanding Role of Mass Spectrometry*

  2004cited by this paper
• The tissue factor/factor VIIa/factor Xa complex: A model built by docking and site‐directed mutagenesis

  2003cited by this paper
• Solution NMR study of the interaction between NTF2 and nucleoporin FxFG repeats.

  2003cited by this paper
• How do helix–helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo‐oligomeric helical bundles

  2003cited by this paper
• Filtering and selection of structural models: Combining docking and NMR

  2003cited by this paper
• Conformation of full‐length Bruton tyrosine kinase (Btk) from synchrotron X‐ray solution scattering

  2003cited by this paper
• The Crystal Structure of the Globular Head of Complement Protein C1q Provides a Basis for Its Versatile Recognition Properties*

  2003cited by this paper
• Exploring Protein–Protein Interactions with Phage Display

  2003cited by this paper
• Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase.

  2003cited by this paper
• Weak alignment offers new NMR opportunities to study protein structure and dynamics

  2003cited by this paper
• Probing the dimeric structure of porcine aminoacylase 1 by mass spectrometric and modeling procedures.

  2003cited by this paper
• Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1H/15N chemical shift mapping and backbone 15N-1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics.

  2003cited by this paper
• DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a

  2003cited by this paper
• Probing catalytically essential domain orientation in histidine kinase EnvZ by targeted disulfide crosslinking.

  2003cited by this paper
• Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin.

  2003cited by this paper
• CAPRI: A Critical Assessment of PRedicted Interactions

  2003cited by this paper
• HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.

  2003cited by this paper
• Assessment of progress over the CASP experiments

  2003cited by this paper
• Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent.

  2003cited by this paper
• Molecular recognition and docking algorithms.

  2003cited by this paper
• Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

  2003cited by this paper
• Taking geometry to its edge: Fast unbound rigid (and hinge‐bent) docking

  2003cited by this paper
• Global orientation of bound MMP-3 and N-TIMP-1 in solution via residual dipolar couplings.

  2003cited by this paper
• Chemical cross-linking and mass spectrometry for protein structural modeling.

  2003cited by this paper
• Protein structure prediction via combinatorial assembly of sub-structural units

  2003cited by this paper
• Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain.

  2003cited by this paper
• Molecular Dissection of the Interaction between the Small G Proteins Rac1 and RhoA and Protein Kinase C-related Kinase 1 (PRK1)*

  2003cited by this paper
• Identification of the protein kinase A regulatory RIα-catalytic subunit interface by amide H/2H exchange and protein docking

  2003cited by this paper
• C2 domain of protein kinase C alpha: elucidation of the membrane docking surface by site-directed fluorescence and spin labeling.

  2003cited by this paper
• Weighted geometric docking: Incorporating external information in the rotation‐translation scan

  2003cited by this paper
• Prediction of the Structure of the Complex Between the 30S Ribosomal Subunit and Colicin E3 via Weighted-Geometric Docking

  2003cited by this paper
• Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.

  2003cited by this paper
• ZDOCK: An initial‐stage protein‐docking algorithm

  2003cited by this paper
• Exploring the conformational space of membrane protein folds matching distance constraints

  2003cited by this paper
• Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans containing more than one cytochrome.

  2003cited by this paper
• Prediction of the multimeric assembly of staphylococcal enterotoxin A with cell-surface protein receptors.

  2003cited by this paper
• An NMR-based Model of the Ubiquitin-bound Human Ubiquitin Conjugation Complex Mms2·Ubc13

  2003cited by this paper
• Breaking symmetry in the structure determination of (large) symmetric protein dimers

  2002cited by this paper
• Experimentally based model of a complex between a snake toxin and the alpha 7 nicotinic receptor.

  2002cited by this paper
• Mapping protein-protein interactions in solution by NMR spectroscopy.

  2002cited by this paper
• Double mutant studies identify electrostatic interactions that are important for docking cytochrome c2 onto the bacterial reaction center.

  2002cited by this paper
• NMR-based determination of the binding epitope and conformational analysis of MUC-1 glycopeptides and peptides bound to the breast cancer-selective monoclonal antibody SM3.

  2002cited by this paper
• MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading

  2002cited by this paper
• Principles of docking: An overview of search algorithms and a guide to scoring functions

  2002cited by this paper
• Structural Model of a Malonyl-CoA-binding Site of Carnitine Octanoyltransferase and Carnitine Palmitoyltransferase I

  2002cited by this paper
• Mining biochemical information: lessons taught by the ribosome.

  2002cited by this paper
• Prediction of protein--protein interaction sites in heterocomplexes with neural networks.

  2002cited by this paper
• Structural clusters of evolutionary trace residues are statistically significant and common in proteins.

  2002cited by this paper
• Evolutionary predictions of binding surfaces and interactions.

  2002cited by this paper
• Solution structure and DNA‐binding properties of the C‐terminal domain of UvrC from E.coli

  2002cited by this paper
• A Structural Model of the Catalytic Subunit-regulatory Subunit Dimeric Complex of the cAMP-dependent Protein Kinase*

  2002cited by this paper
• Unraveling hot spots in binding interfaces: progress and challenges.

  2002cited by this paper

• Structural Analysis of Proteins from Bacterial Secretion Systems and Their Assemblies by NMR Spectroscopy.

  2024cites this paper
• Comparison of human FTO and mutant R322Q with various ligands for poly malformation syndrome treatment

  2024cites this paper
• Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

  2021cites this paper
• Selective Binding of Small Molecules to Vibrio cholerae DsbA Offers a Starting Point for the Design of Novel Antibacterials

  2021cites this paper
• Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β‐catenin and TRIB pseudokinases

  2021cites this paper
• Protein-Protein Modeling Using Cryo-EM Restraints.

  2020cites this paper
• Desarrollo bioinformático y modelado in-silico para el análisis del ajuste inducido en las enzimas citocromo P450

  2019cites this paper
• Structural basis of βTrCP1-associated GLI3 processing

  2019cites this paper
• Peptide science: a "rule model" for new generations of peptidomimetics.

  2019cites this paper
• Integrative Structure Modeling: Overview and Assessment.

  2019cites this paper
• Protein Docking and Drug Design

  2019cites this paper
• General MS 3 D modelling procedures 2 . 1 Possible computational protocols for MS 3 D approaches

  2018cites this paper
• A Dynamic Overview of Antimicrobial Peptides and Their Complexes

  2018cites this paper
• Recognition of Nucleosomes by Chromatin Factors: Lessons from Data-Driven Docking-Based Structures of Nucleosome-Protein Complexes

  2018cites this paper
• Chemical shift-based methods in NMR structure determination.

  2018cites this paper
• Cytochrome c speeds up caspase cascade activation by blocking 14-3-3ε-dependent Apaf-1 inhibition

  2018cites this paper
• High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization.

  2017cites this paper
• Increased hydrophobic surface exposure in the cataract-related G18V variant of human γS-crystallin.

  2016cites this paper
• Multidrug efflux pumps and their inhibitors characterized by computational modeling

  2016cites this paper
• Determination of ligand binding modes in weak protein–ligand complexes using sparse NMR data

  2016cites this paper
• Resolution of protein structure by mass spectrometry.

  2016cites this paper
• Computational Drug Repositioning by Target Hopping: A Use Case in Chagas Disease.

  2016cites this paper
• Understanding the Molecular Basis of Transparency and Refraction in the Eye Lens

  2016cites this paper
• Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.

  2016cites this paper
• Elucidation, functional clustering and structural characterization of βTrCP1 substrates through a molecular dynamics study.

  2016cites this paper
• Homology modeling and docking study of Danio rerio Carbonic Anhydrase VI - Pentraxin protein and bioinformatics analysis of extra-cellular CAs

  2015cites this paper
• How Important is to Account for Water When Modeling Biomolecular Complexes

  2015cites this paper
• A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy.

  2015cites this paper
• Molecular docking uncovers TSPY binds more efficiently with eEF1A2 compared to eEF1A1

  2015cites this paper
• New Computational Methods to Calculate Drug-Receptor Binding Free Energies

  2015cites this paper
• Information-driven modeling of protein-peptide complexes.

  2015cites this paper
• Integrative computational modeling of protein interactions

  2014cites this paper
• Cytochrome c1 exhibits two binding sites for cytochrome c in plants.

  2014influential citation
• Protein Binding Site Similarities as Driver for Drug Repositioning

  2014cites this paper
• Computational Structural Biology of Macromolecular Interactions

  2014cites this paper
• Molecular dynamics and regulation of butyrylcholinesterase cholinergic activity by RNA binding proteins.

  2014cites this paper
• Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis

  2014cites this paper
• Interactions of HIV-1 proteins with their cellular partners : insights from computational methods

  2013cites this paper
• Protein-ligand docking in the new millennium--a retrospective of 10 years in the field.

  2013cites this paper
• Solvated protein–DNA docking using HADDOCK

  2013cites this paper
• Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

  2013cites this paper
• Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes.

  2013cites this paper
• Structure prediction and molecular dynamics simulations of a G-protein coupled receptor: human CCR2 receptor

  2013cites this paper
• Structural Bioinformatics and Protein Docking Analysis of the Molecular Chaperone-Kinase Interactions: Towards Allosteric Inhibition of Protein Kinases by Targeting the Hsp90-Cdc37 Chaperone Machinery

  2013cites this paper
• Advances in integrative modeling of biomolecular complexes.

  2013cites this paper
• Prediction of Protein-Protein Binding Interfaces

  2013cites this paper
• In silico study of protein-protein interactions

  2013cites this paper
• Solvated protein–protein docking using Kyte‐Doolittle‐based water preferences

  2013cites this paper
• Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12

  2013cites this paper
• NMR studies of weak protein-protein interactions.

  2013cites this paper
• KBDOCK 2013: a spatial classification of 3D protein domain family interactions

  2013cites this paper
• Protein docking using case‐based reasoning

  2013cites this paper
• Characterization of the Membrane-Bound Full-Length Complex between Cytochrome b5 and Cytochrome P450 2B4.

  2013cites this paper
• Development of enrichment methods for cross-linked peptides to study the dynamic topology of large protein complexes by mass spectrometry

  2013cites this paper
• Synergistic Applications of MD and NMR for the Study of Biological Systems

  2012cites this paper
• Predicting Protein Complex Structures : A Review of the Docking Process

  2012cites this paper
• On the use of distance constraints in protein–protein docking computations

  2012cites this paper
• A Critical Assessment of Information-guided Protein–Protein Docking Predictions*

  2012cites this paper
• Mapping of discontinuous conformational epitopes by amide hydrogen/deuterium exchange mass spectrometry and computational docking

  2012cites this paper
• Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry.

  2012cites this paper
• Knowledge-based Approaches for Modelling the 3D Structural Interactome. (Extraction de Connaissances pour la Modelisation tri-dimensionnelle de l'Interactome Structural)

  2012cites this paper
• Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.

  2012cites this paper
• platelet receptor GPVI receptor LAIR-1: unexpected implications for collagen binding by Crystal structure and collagen-binding site of immune inhibitory

  2012cites this paper
• Probing Noncovalent Interactions by Electrospray Ionization and Matrix‐Assisted Laser Desorption/Ionization

  2012cites this paper
• 15 Predicting and Dissecting High-order Molecular Complexity by Information-driven Biomolecular Docking

  2012cites this paper
• Antimicrobial activity of carbon nanotubes.

  2012cites this paper
• CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

  2011cites this paper
• Spatial clustering of protein binding sites for template based protein docking

  2011cites this paper
• Structural Model of Ligand-G Protein-coupled Receptor (GPCR) Complex Based on Experimental Double Mutant Cycle Data

  2011cites this paper
• Methods for hybrid modeling of solution scattering data and their applications

  2011cites this paper
• Computational Methods in Mass Spectrometry-Based Protein 3D Studies

  2011cites this paper
• The Biflavonoid Amentoflavone Inhibits Neovascularization Preventing the Activity of Proangiogenic Vascular Endothelial Growth Factors*

  2011cites this paper
• Low‐resolution structural approaches to study biomolecular assemblies

  2011cites this paper
• Spezifische Proteinerkennung durch Array‐gebundene Hexanukleotide

  2011cites this paper
• Structure determination of a protein assembly by amino acid selective cross‐saturation

  2011cites this paper
• A small-molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments.

  2011cites this paper
• A novel ErbB2 epitope targeted by human antitumor immunoagents

  2011cites this paper
• The HADDOCK web server for data-driven biomolecular docking

  2010cites this paper
• Stabilisierung eines niederaffinen Zustands für Effektoren im menschlichen Ras-Protein durch Cyclenkomplexe

  2010cites this paper
• Structural studies of nucleic acids and proteins involved in nucleic acid recognition

  2010cites this paper
• Specific Recognition of Proteins by Array‐Bound Hexanucleotides†

  2010cites this paper
• Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions

  2010cites this paper
• A Docking Model Based on Mass Spectrometric and Biochemical Data Describes Phage Packaging Motor Incorporation*

  2010cites this paper
• Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes.

  2010cites this paper
• Crystal structure and collagen-binding site of immune inhibitory receptor LAIR-1: unexpected implications for collagen binding by platelet receptor GPVI.

  2010cites this paper
• Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance

  2010cites this paper
• Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density

  2010cites this paper
• Homology modeling of G-protein-coupled receptors with X-ray structures on the rise.

  2010cites this paper
• Using Solid Angles to Detect Protein Docking Regions by CUDA Parallel Algorithms

  2010cites this paper
• Molecular characterization and evolutionary plasticity of protein-protein interfaces

  2010cites this paper
• Use of quantitative 1H NMR chemical shift changes for ligand docking into barnase

  2009cites this paper
• Ras classical effectors: new tales from in silico complexes.

  2009cites this paper
• Combining interface core and whole interface descriptors in postscan processing of protein‐protein docking models

  2009influential citation
• Protein–protein docking dealing with the unknown

  2009cites this paper
• Surveying ubiquitin structure by noncovalent attachment of distance constrained bis(crown) ethers.

  2008cites this paper
• Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes.

  2008cites this paper
• Influence of conformational flexibility on complexation-induced changes in chemical shift in a neocarzinostatin protein-ligand complex.

  2008cites this paper
• Recent progress and future directions in protein-protein docking.

  2008influential citation
• Determination of protein-ligand binding modes using complexation-induced changes in (1)h NMR chemical shift.

  2008cites this paper
• Integrating diverse data for structure determination of macromolecular assemblies.

  2008cites this paper