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HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

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What this work says

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

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CAPRI: A Critical Assessment of PRedicted Interactions

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Assessment of blind predictions of protein–protein interactions: Current status of docking methods

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Various strategies of using residual dipolar couplings in NMR‐driven protein docking: Application to Lys48‐linked di‐ubiquitin and validation against 15 N‐relaxation data

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Prediction of interface residues in protein–protein complexes by a consensus neural network method: Test against NMR data

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Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures

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Data‐driven docking: HADDOCK's adventures in CAPRI

inferredcites →https://doi.org/10.1002/prot.20842openalex-snapshot

WHISCY: What information does surface conservation yield? Application to data‐driven docking

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Combining NMR Relaxation with Chemical Shift Perturbation Data to Drive Protein–protein Docking

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WHAT IF: A molecular modeling and drug design program

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Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes

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ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites

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Crystal Structure of the Complex between the Monomeric Form of Toxoplasma gondii Surface Antigen 1 (SAG1) and a Monoclonal Antibody that Mimics the Human Immune Response

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Structural Basis for the Bifunctionality of the U5 snRNP 52K Protein (CD2BP2)

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Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC

inferredcites →https://doi.org/10.1016/j.sbi.2006.02.002openalex-snapshot

Flexible protein–protein docking

inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot

High-resolution protein–protein docking

inferredcites →https://doi.org/10.1016/j.tibtech.2004.01.006openalex-snapshot

Protein–protein docking: is the glass half-full or half-empty?

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Modeller: Generation and Refinement of Homology-Based Protein Structure Models

inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

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Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein

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Activity–structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16

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SWISS-MODEL: an automated protein homology-modeling server

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Protein structure prediction and analysis using the Robetta server

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Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

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PRODRG: a tool for high-throughput crystallography of protein–ligand complexes

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Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

inferredcites →https://doi.org/10.1110/ps.041081905openalex-snapshot

Assessing predictions of protein–protein interaction: The CAPRI experiment

inferredcites →https://doi.org/10.1111/j.1742-4658.2004.04473.xopenalex-snapshot

Data‐driven docking for the study of biomolecular complexes

What points at this work

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

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Protein Structure Calculation using Ambiguous Restraints

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Assessing Structural Predictions of Protein–Protein Recognition: The CAPRI Experiment

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Nuclear Magnetic Resonance of Amino Acids, Peptides, and Proteins

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Protein–Protein Docking with HADDOCK

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Cytochrome c1 exhibits two binding sites for cytochrome c in plants

inferred← citeshttps://doi.org/10.1016/j.bbagen.2010.11.001openalex-snapshot

Human galectin-3 (Mac-2 antigen): Defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region

inferred← citeshttps://doi.org/10.1016/j.bbagen.2017.08.020openalex-snapshot

Solution NMR views of dynamical ordering of biomacromolecules

inferred← citeshttps://doi.org/10.1016/j.bbapap.2013.11.008openalex-snapshot

Structural and biochemical analyses of Microcystis aeruginosa O-acetylserine sulfhydrylases reveal a negative feedback regulation of cysteine biosynthesis

inferred← citeshttps://doi.org/10.1016/j.bbapap.2014.06.016openalex-snapshot

Molecular landscape of the interaction between the urease accessory proteins UreE and UreG

inferred← citeshttps://doi.org/10.1016/j.bbapap.2014.06.017openalex-snapshot

Interaction of S100A13 with C2 domain of receptor for advanced glycation end products (RAGE)

inferred← citeshttps://doi.org/10.1016/j.bbapap.2014.08.002openalex-snapshot

NMR characterization of the electrostatic interaction of the basic residues in HDGF and FGF2 during heparin binding

inferred← citeshttps://doi.org/10.1016/j.bbapap.2014.09.020openalex-snapshot

Crystal structure of HlyU, the hemolysin gene transcription activator, from Vibrio cholerae N16961 and functional implications

inferred← citeshttps://doi.org/10.1016/j.bbrc.2010.10.089openalex-snapshot

The NMR solution structure of human epidermal growth factor (hEGF) at physiological pH and its interactions with suramin

inferred← citeshttps://doi.org/10.1016/j.bbrc.2015.10.036openalex-snapshot

Characterization of the interaction between Escherichia coli topoisomerase IV E subunit and an ATP competitive inhibitor

inferred← citeshttps://doi.org/10.1016/j.bbrc.2019.11.088openalex-snapshot

ATP is a cryptic binder of TDP-43 RRM domains to enhance stability and inhibit ALS/AD-associated fibrillation

inferred← citeshttps://doi.org/10.1016/j.bbrc.2019.11.180openalex-snapshot

ATP binds nucleic-acid-binding domains beyond RRM fold

inferred← citeshttps://doi.org/10.1016/j.bbrc.2021.01.018openalex-snapshot

ATP biphasically modulates LLPS of SARS-CoV-2 nucleocapsid protein and specifically binds its RNA-binding domain

inferred← citeshttps://doi.org/10.1016/j.bbrep.2015.12.002openalex-snapshot

Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor – An Insight through molecular dynamics and docking approach

inferred← citeshttps://doi.org/10.1016/j.biocel.2016.04.004openalex-snapshot

Structural modeling of G-protein coupled receptors: An overview on automatic web-servers

inferred← citeshttps://doi.org/10.1016/j.biologicals.2015.07.008openalex-snapshot

Rational design of stable and functional hirudin III mutants with lower antigenicity

inferred← citeshttps://doi.org/10.1016/j.bpj.2010.01.052openalex-snapshot

The Folding Transition-State Ensemble of a Four-Helix Bundle Protein: Helix Propensity as a Determinant and Macromolecular Crowding as a Probe

inferred← citeshttps://doi.org/10.1016/j.bpj.2015.12.038openalex-snapshot

Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

inferred← citeshttps://doi.org/10.1016/j.bpj.2016.07.001openalex-snapshot

Structure of an Intrinsically Disordered Stress Protein Alone and Bound to a Membrane Surface

inferred← citeshttps://doi.org/10.1016/j.bpj.2017.12.030openalex-snapshot

Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail

inferred← citeshttps://doi.org/10.1016/j.bpj.2018.01.045openalex-snapshot

Modeling the Early Stages of Phase Separation in Disordered Elastin-like Proteins

inferred← citeshttps://doi.org/10.1016/j.carbpol.2020.117038openalex-snapshot

Structural insights in interactions between RNase from Bacillus Intermedius and rhamnogalacturonan I from potato

inferred← citeshttps://doi.org/10.1016/j.carbpol.2020.117181openalex-snapshot

Interaction-induced structural transformation of lysozyme and kappa-carrageenan in binary complexes

inferred← citeshttps://doi.org/10.1016/j.ccr.2014.05.007openalex-snapshot

Transient iron coordination sites in proteins: Exploiting the dual nature of paramagnetic NMR

inferred← citeshttps://doi.org/10.1016/j.cell.2011.01.035openalex-snapshot

The Mechanism of Linkage-Specific Ubiquitin Chain Elongation by a Single-Subunit E2

inferred← citeshttps://doi.org/10.1016/j.cell.2016.03.045openalex-snapshot

A Small Molecule RAS-Mimetic Disrupts RAS Association with Effector Proteins to Block Signaling

inferred← citeshttps://doi.org/10.1016/j.cellsig.2014.11.036openalex-snapshot

Structural perspective of ARHI mediated inhibition of STAT3 signaling: An insight into the inactive to active transition of ARHI and its interaction with STAT3 and importinβ

inferred← citeshttps://doi.org/10.1016/j.celrep.2012.10.010openalex-snapshot

Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface

inferred← citeshttps://doi.org/10.1016/j.celrep.2022.110449openalex-snapshot

Epitope length variants balance protective immune responses and viral escape in HIV-1 infection

inferred← citeshttps://doi.org/10.1016/j.celrep.2024.114334openalex-snapshot

Tentonin 3 is a pore-forming subunit of a slow inactivation mechanosensitive channel

inferred← citeshttps://doi.org/10.1016/j.chembiol.2013.11.014openalex-snapshot

Design and Synthesis of Truncated EGF-A Peptides that Restore LDL-R Recycling in the Presence of PCSK9 In Vitro

inferred← citeshttps://doi.org/10.1016/j.chom.2020.06.021openalex-snapshot

Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2

inferred← citeshttps://doi.org/10.1016/j.chroma.2016.03.087openalex-snapshot

Design of protease-resistant peptide ligands for the purification of antibodies from human plasma

inferred← citeshttps://doi.org/10.1016/j.chroma.2024.464912openalex-snapshot

Identification of a broad-spectrum high-affinity peptide ligand for the purification of spike proteins

inferred← citeshttps://doi.org/10.1016/j.chroma.2025.465937openalex-snapshot

De novo design and discovery of broad-spectrum affinity peptide ligands for influenza A vaccines

inferred← citeshttps://doi.org/10.1016/j.chroma.2025.466552openalex-snapshot

Discovery of a broad-spectrum affibody ligand for COVID-19 vaccine purification

inferred← citeshttps://doi.org/10.1016/j.chroma.2026.467271openalex-snapshot

Leveraging protein language model for maturation of high-affinity peptide ligand in the purification of an adeno‒associated virus vector

inferred← citeshttps://doi.org/10.1016/j.colcom.2026.100923openalex-snapshot

Computationally guided engineering of an aptamer–gold nanoparticle aptasensor for ultrasensitive detection of α-synuclein in biological matrices

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2016.01.009openalex-snapshot

Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase

inferred← citeshttps://doi.org/10.1016/j.csbj.2017.01.003openalex-snapshot

Biobetters From an Integrated Computational/Experimental Approach

inferred← citeshttps://doi.org/10.1016/j.csbj.2019.12.002openalex-snapshot

A protocol to automatically calculate homo-oligomeric protein structures through the integration of evolutionary constraints and NMR ambiguous contacts

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.09.003openalex-snapshot

Predicting stable binding modes from simulated dimers of the D76N mutant of β2-microglobulin

inferred← citeshttps://doi.org/10.1016/j.cub.2018.10.002openalex-snapshot

Distinct Interaction Sites of Rac GTPase with WAVE Regulatory Complex Have Non-redundant Functions in Vivo

inferred← citeshttps://doi.org/10.1016/j.drudis.2014.02.005openalex-snapshot

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

inferred← citeshttps://doi.org/10.1016/j.febslet.2008.11.037openalex-snapshot

NMR structural characterization of the penta‐peptide calpain inhibitor

inferred← citeshttps://doi.org/10.1016/j.febslet.2010.10.033openalex-snapshot

Interaction between separated consecutive complement control modules of human C1r: Implications for dimerization of the full‐length protease

inferred← citeshttps://doi.org/10.1016/j.febslet.2012.03.027openalex-snapshot

NMR characterization of the interaction between the PUB domain of peptide:N‐glycanase and ubiquitin‐like domain of HR23

inferred← citeshttps://doi.org/10.1016/j.febslet.2012.04.063openalex-snapshot

PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2

inferred← citeshttps://doi.org/10.1016/j.febslet.2013.07.021openalex-snapshot

Structural basis for recognition of the third SH3 domain of full‐length R85 (R85FL)/ponsin by ataxin‐7

inferred← citeshttps://doi.org/10.1016/j.ibmb.2017.08.004openalex-snapshot

Active subsite properties, subsite residues and targeting to lysosomes or midgut lumen of cathepsins L from the beetle Tenebrio molitor

inferred← citeshttps://doi.org/10.1016/j.ibmb.2020.103488openalex-snapshot

Cathepsins L and B in Dysdercus peruvianus, Rhodnius prolixus, and Mahanarva fimbriolata. Looking for enzyme adaptations to digestion

inferred← citeshttps://doi.org/10.1016/j.intimp.2017.04.028openalex-snapshot

Heterotrimeric complex of p38 MAPK, PKCδ, and TIRAP is required for AP1 mediated inflammatory response

inferred← citeshttps://doi.org/10.1016/j.jbc.2022.102454openalex-snapshot

High-resolution structures of a siderophore-producing cyclization domain from Yersinia pestis offer a refined proposal of substrate binding

inferred← citeshttps://doi.org/10.1016/j.jinf.2020.02.026openalex-snapshot

COVID-19 spike-host cell receptor GRP78 binding site prediction

inferred← citeshttps://doi.org/10.1016/j.jmb.2008.05.042openalex-snapshot

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

inferred← citeshttps://doi.org/10.1016/j.jmb.2008.12.005openalex-snapshot

Epitope Mapping of a Bactericidal Monoclonal Antibody against the Factor H Binding Protein of Neisseria meningitidis

inferred← citeshttps://doi.org/10.1016/j.jmb.2009.03.001openalex-snapshot

An Efficient Strategy for the Determination of the Three-Dimensional Architecture of Ribonucleoprotein Complexes by the Combination of a Few Easily Accessible NMR and Biochemical Data: Intermolecular Recognition in a U4 Spliceosomal Complex

inferred← citeshttps://doi.org/10.1016/j.jmb.2009.05.022openalex-snapshot

Specificity and Affinity of Lac Repressor for the Auxiliary Operators O2 and O3 Are Explained by the Structures of Their Protein–DNA Complexes

inferred← citeshttps://doi.org/10.1016/j.jmb.2009.05.063openalex-snapshot

Nonmyristoylated Matrix Protein from the Mason–Pfizer Monkey Virus Forms Oligomers

inferred← citeshttps://doi.org/10.1016/j.jmb.2009.10.039openalex-snapshot

Exploring the Linkage Dependence of Polyubiquitin Conformations Using Molecular Modeling

inferred← citeshttps://doi.org/10.1016/j.jmb.2010.05.035openalex-snapshot

Structural Evidence for the Functional Importance of the Heme Domain Mobility in Flavocytochrome b2

inferred← citeshttps://doi.org/10.1016/j.jmb.2010.10.005openalex-snapshot

Delineation of the Complement Receptor Type 2–C3d Complex by Site-Directed Mutagenesis and Molecular Docking

inferred← citeshttps://doi.org/10.1016/j.jmb.2012.07.021openalex-snapshot

The Structure of Myristoylated Mason-Pfizer Monkey Virus Matrix Protein and the Role of Phosphatidylinositol-(4,5)-Bisphosphate in Its Membrane Binding

inferred← citeshttps://doi.org/10.1016/j.jmb.2015.09.014openalex-snapshot

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

inferred← citeshttps://doi.org/10.1016/j.jmb.2016.07.025openalex-snapshot

Structure and Function of the RING Domains of RNF20 and RNF40, Dimeric E3 Ligases that Monoubiquitylate Histone H2B

inferred← citeshttps://doi.org/10.1016/j.jmb.2016.08.016openalex-snapshot

A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome

inferred← citeshttps://doi.org/10.1016/j.jmb.2016.10.002openalex-snapshot

NMR Reveals the Interplay among the AMSH SH3 Binding Motif, STAM2, and Lys63-Linked Diubiquitin

inferred← citeshttps://doi.org/10.1016/j.jmb.2017.05.005openalex-snapshot

Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints

inferred← citeshttps://doi.org/10.1016/j.jmb.2018.02.002openalex-snapshot

The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism

inferred← citeshttps://doi.org/10.1016/j.jmb.2019.10.019openalex-snapshot

CD8 Binding of MHC-Peptide Complexes in cis or trans Regulates CD8+ T-cell Responses

inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.09.004openalex-snapshot

Structural analysis of the woodland strawberry COI1-JAZ1 co-receptor for the plant hormone jasmonoyl-isoleucine

inferred← citeshttps://doi.org/10.1016/j.jmgm.2020.107804openalex-snapshot

Structure based peptide design, molecular dynamics and MM-PBSA studies for targeting C terminal dimerization of NFAT5 DNA binding domain

inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108502openalex-snapshot

Molecular dynamics simulation of the interaction of a raspberry polygalacturonase (RiPG) with a PG inhibiting protein (RiPGIP) isolated from ripening raspberry (Rubus idaeus cv. Heritage) fruit as a model to understand proteins interaction during fruit softening

inferred← citeshttps://doi.org/10.1016/j.jmr.2013.10.021openalex-snapshot

Information-driven modeling of large macromolecular assemblies using NMR data

inferred← citeshttps://doi.org/10.1016/j.jsb.2009.07.011openalex-snapshot

Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis

inferred← citeshttps://doi.org/10.1016/j.jsb.2010.09.004openalex-snapshot

Three-dimensional molecular modeling with single molecule FRET

inferred← citeshttps://doi.org/10.1016/j.jsb.2010.11.004openalex-snapshot

NMR and small-angle scattering-based structural analysis of protein complexes in solution

inferred← citeshttps://doi.org/10.1016/j.jsb.2010.11.005openalex-snapshot

Structural NMR of protein oligomers using hybrid methods

inferred← citeshttps://doi.org/10.1016/j.jsb.2011.04.001openalex-snapshot

Rapid identification of protein–protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements

inferred← citeshttps://doi.org/10.1016/j.jsb.2013.03.004openalex-snapshot

Interactions of the α-subunits of heterotrimeric G-proteins with GPCRs, effectors and RGS proteins: A critical review and analysis of interacting surfaces, conformational shifts, structural diversity and electrostatic potentials

inferred← citeshttps://doi.org/10.1016/j.molcel.2010.10.018openalex-snapshot

WD40 Repeat Propellers Define a Ubiquitin-Binding Domain that Regulates Turnover of F Box Proteins

inferred← citeshttps://doi.org/10.1016/j.molcel.2014.04.004openalex-snapshot

Accessibility of Different Histone H3-Binding Domains of UHRF1 Is Allosterically Regulated by Phosphatidylinositol 5-Phosphate

inferred← citeshttps://doi.org/10.1016/j.molcel.2014.09.009openalex-snapshot

Mechanism of Polyubiquitination by Human Anaphase-Promoting Complex: RING Repurposing for Ubiquitin Chain Assembly

inferred← citeshttps://doi.org/10.1016/j.nano.2013.11.006openalex-snapshot

Sheltering DNA in self-organizing, protein-only nano-shells as artificial viruses for gene delivery

inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2016.09.008openalex-snapshot

Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes

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