On the public citation graph

The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI

https://doi.org/10.1002/prot.21747
0 signed · 103 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/prot.10092openalex-snapshot
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
inferredcites →https://doi.org/10.1002/prot.10334openalex-snapshot
A novel shape complementarity scoring function for protein‐protein docking
inferredcites →https://doi.org/10.1002/prot.10388openalex-snapshot
ZDOCK predictions for the CAPRI challenge
inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.10393openalex-snapshot
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
inferredcites →https://doi.org/10.1002/prot.1168openalex-snapshot
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
inferredcites →https://doi.org/10.1002/prot.20551openalex-snapshot
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
inferredcites →https://doi.org/10.1002/prot.20559openalex-snapshot
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
inferredcites →https://doi.org/10.1002/prot.20560openalex-snapshot
Protein–protein docking benchmark 2.0: An update
inferredcites →https://doi.org/10.1002/prot.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21502openalex-snapshot
Integrating statistical pair potentials into protein complex prediction
inferredcites →https://doi.org/10.1006/jmbi.1996.0859openalex-snapshot
Determination of atomic desolvation energies from the structures of crystallized proteins
inferredcites →https://doi.org/10.1016/j.jmb.2004.05.019openalex-snapshot
Structural Characterization and Comparative Phylogenetic Analysis of Escherichia coli HemK, a Protein (N5)-glutamine Methyltransferase
inferredcites →https://doi.org/10.1016/j.molcel.2005.10.025openalex-snapshot
Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC
inferredcites →https://doi.org/10.1016/j.str.2004.03.021openalex-snapshot
Crystal Structure of the DH/PH Fragment of Dbs without Bound GTPase
inferredcites →https://doi.org/10.1016/s0022-2836(03)00670-3openalex-snapshot
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
inferredcites →https://doi.org/10.1016/s0092-8674(02)00630-xopenalex-snapshot
Structural Basis for E2-Mediated SUMO Conjugation Revealed by a Complex between Ubiquitin-Conjugating Enzyme Ubc9 and RanGAP1
inferredcites →https://doi.org/10.1021/bi034026popenalex-snapshot
Structures along the Catalytic Pathway of PrmC/HemK, an N 5 -Glutamine AdoMet-Dependent Methyltransferase
inferredcites →https://doi.org/10.1021/ja070153nopenalex-snapshot
Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein
inferredcites →https://doi.org/10.1038/nature03588openalex-snapshot
Insights into E3 ligase activity revealed by a SUMO–RanGAP1–Ubc9–Nup358 complex
inferredcites →https://doi.org/10.1038/nsmb1104openalex-snapshot
Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway
inferredcites →https://doi.org/10.1038/nsmb903openalex-snapshot
SUMO modification of the ubiquitin-conjugating enzyme E2-25K
inferredcites →https://doi.org/10.1038/sj.emboj.7601634openalex-snapshot
Structural basis for ARF1‐mediated recruitment of ARHGAP21 to Golgi membranes
inferredcites →https://doi.org/10.1046/j.1365-2958.1998.00945.xopenalex-snapshot
TolB protein ofEscherichia coliK‐12 interacts with the outer membrane peptidoglycan‐associated proteins Pal, Lpp and OmpA
inferredcites →https://doi.org/10.1073/pnas.0503525102openalex-snapshot
Structural basis of the Sir1–origin recognition complex interaction in transcriptional silencing
inferredcites →https://doi.org/10.1074/jbc.272.34.21381openalex-snapshot
Crystal Structure of Murine/Human Ubc9 Provides Insight into the Variability of the Ubiquitin-conjugating System
inferredcites →https://doi.org/10.1093/bioinformatics/bti229openalex-snapshot
M-ZDOCK: a grid-based approach for Cn symmetric multimer docking
inferredcites →https://doi.org/10.1093/emboj/21.4.769openalex-snapshot
The hemK gene in Escherichia coli encodes the N5‐glutamine methyltransferase that modifies peptide release factors
inferredcites →https://doi.org/10.1093/emboj/21.6.1315openalex-snapshot
A crystallographic view of interactions between Dbs and Cdc42: PH domain‐assisted guanine nucleotide exchange
inferredcites →https://doi.org/10.1093/emboj/cdf468openalex-snapshot
Structure and function of the BAH‐containing domain of Orc1p in epigenetic silencing
inferredcites →https://doi.org/10.1093/genetics/151.1.31openalex-snapshot
A Region of the Sir1 Protein Dedicated to Recognition of a Silencer and Required for Interaction with the Orc1 Protein in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkh468openalex-snapshot
Protein structure prediction and analysis using the Robetta server
inferredcites →https://doi.org/10.1126/science.1062023openalex-snapshot
The Guanine Nucleotide-Binding Switch in Three Dimensions
inferredcites →https://doi.org/10.1128/jb.182.3.821-824.2000openalex-snapshot
Identification by Genetic Suppression of Escherichia coli TolB Residues Important for TolB-Pal Interaction

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118889886.ch4openalex-snapshot
Assessing Structural Predictions of Protein–Protein Recognition: The CAPRI Experiment
inferred← citeshttps://doi.org/10.1002/jcc.21276openalex-snapshot
Protein–protein docking dealing with the unknown
inferred← citeshttps://doi.org/10.1002/jmr.2237openalex-snapshot
Mapping discontinuous protein‐binding sites via structure‐based peptide libraries: combiningin silicoandin vitroapproaches
inferred← citeshttps://doi.org/10.1002/pmic.201000283openalex-snapshot
Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint‐based docking
inferred← citeshttps://doi.org/10.1002/pro.2181openalex-snapshot
A flexible docking approach for prediction of T cell receptor–peptide–MHC complexes
inferred← citeshttps://doi.org/10.1002/pro.687openalex-snapshot
Integrating atom‐based and residue‐based scoring functions for protein–protein docking
inferred← citeshttps://doi.org/10.1002/prot.21920openalex-snapshot
A combination of rescoring and refinement significantly improves protein docking performance
inferred← citeshttps://doi.org/10.1002/prot.22309openalex-snapshot
Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking
inferred← citeshttps://doi.org/10.1002/prot.22343openalex-snapshot
Refining near‐native protein–protein docking decoys by local resampling and energy minimization
inferred← citeshttps://doi.org/10.1002/prot.22764openalex-snapshot
Performance of ZDOCK and ZRANK in CAPRI rounds 13–19
inferred← citeshttps://doi.org/10.1002/prot.22844openalex-snapshot
How different from random are docking predictions when ranked by scoring functions?
inferred← citeshttps://doi.org/10.1002/prot.23070openalex-snapshot
A machine learning approach for the prediction of protein surface loop flexibility
inferred← citeshttps://doi.org/10.1002/prot.24432openalex-snapshot
Performance of ZDOCK in CAPRI rounds 20–26
inferred← citeshttps://doi.org/10.1002/prot.25186openalex-snapshot
Performance of ZDOCK and IRAD in CAPRI rounds 28–34
inferred← citeshttps://doi.org/10.1002/prot.25234openalex-snapshot
Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking
inferred← citeshttps://doi.org/10.1002/prot.25873openalex-snapshot
Performance of ZDOCK and IRAD in CAPRI rounds 39‐45
inferred← citeshttps://doi.org/10.1002/prot.26801openalex-snapshot
AlphaFold and Docking Approaches for Antibody–Antigen and Other Targets: Insights From CAPRI Rounds 47–55
inferred← citeshttps://doi.org/10.1007/978-1-60327-241-4_20openalex-snapshot
Analysis and Prediction of Protein Quaternary Structure
inferred← citeshttps://doi.org/10.1007/978-94-007-5285-6_6openalex-snapshot
Prediction of Protein-Protein Binding Interfaces
inferred← citeshttps://doi.org/10.1007/s00894-011-0982-yopenalex-snapshot
A computerized protein–protein interaction modeling study of ampicillin antibody specificity in relation to biosensor development
inferred← citeshttps://doi.org/10.1007/s00894-020-04524-zopenalex-snapshot
In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus
inferred← citeshttps://doi.org/10.1007/s10930-020-09959-0openalex-snapshot
HNF1A-MODY Mutations in Nuclear Localization Signal Impair HNF1A-Import Receptor KPNA6 Interactions
inferred← citeshttps://doi.org/10.1007/s12010-013-0342-8openalex-snapshot
Molecular Dynamic and Docking Interaction Study of Heterodera glycines Serine Proteinase with Vigna mungo Proteinase Inhibitor
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.2015.05.019openalex-snapshot
Cross‐linking analysis reveals the putative dimer structure of the cyanobacterial BLUF photoreceptor PixD
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.jmgm.2011.11.001openalex-snapshot
Molecular modeling of Bt Cry1Ac (DI–DII)–ASAL (Allium sativum lectin)–fusion protein and its interaction with aminopeptidase N (APN) receptor of Manduca sexta
inferred← citeshttps://doi.org/10.1016/j.sbi.2009.02.008openalex-snapshot
Convergence and combination of methods in protein–protein docking
inferred← citeshttps://doi.org/10.1016/j.str.2011.04.006openalex-snapshot
Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination
inferred← citeshttps://doi.org/10.1016/j.talanta.2025.127834openalex-snapshot
Magnetic-assisted and aptamer-based SERS biosensor for high enrichment, ultrasensitive detection of multicomponent heart failure biomarkers
inferred← citeshttps://doi.org/10.1021/acs.biochem.6b00263openalex-snapshot
Photochemical Reactions of the LOV and LOV-Linker Domains of the Blue Light Sensor Protein YtvA
inferred← citeshttps://doi.org/10.1021/bi101448topenalex-snapshot
Biochemical and Physiological Characterization of a BLUF Protein−EAL Protein Complex Involved in Blue Light-Dependent Degradation of Cyclic Diguanylate in the Purple Bacterium Rhodopseudomonas palustris
inferred← citeshttps://doi.org/10.1021/bi301004vopenalex-snapshot
A Predicted Structure for the PixD–PixE Complex Determined by Homology Modeling, Docking Simulations, and a Mutagenesis Study
inferred← citeshttps://doi.org/10.1021/jp108397aopenalex-snapshot
Delocalization-Enhanced Long-Range Energy Transfer between Cryptophyte Algae PE545 Antenna Proteins
inferred← citeshttps://doi.org/10.1038/nature08613openalex-snapshot
A gate–latch–lock mechanism for hormone signalling by abscisic acid receptors
inferred← citeshttps://doi.org/10.1038/nprot.2010.32openalex-snapshot
The HADDOCK web server for data-driven biomolecular docking
inferred← citeshttps://doi.org/10.1039/c005293kopenalex-snapshot
A novel class of protease targets of phosphatidylethanolamine-binding proteins (PEBP): a study of the acylpeptide hydrolase and the PEBPinhibitor from the archaeon Sulfolobus solfataricus
inferred← citeshttps://doi.org/10.1074/jbc.m111.280149openalex-snapshot
Structural Determinants of Caspase-9 Inhibition by the Vaccinia Virus Protein, F1L
inferred← citeshttps://doi.org/10.1074/jbc.m112.436576openalex-snapshot
Water-soluble LYNX1 Residues Important for Interaction with Muscle-type and/or Neuronal Nicotinic Receptors
inferred← citeshttps://doi.org/10.1080/07391102.2018.1526712openalex-snapshot
Mechanistic insights into high mobility group box-1 (HMGb1)-induced Toll-like receptor 4 (TLR4) dimer formation
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu097openalex-snapshot
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
inferred← citeshttps://doi.org/10.1093/nar/gkn216openalex-snapshot
The RosettaDock server for local protein-protein docking
inferred← citeshttps://doi.org/10.1093/pcp/pcs108openalex-snapshot
A PixD—PapB Chimeric Protein Reveals the Function of the BLUF Domain C-Terminal α-Helices for Light Signal Transduction
inferred← citeshttps://doi.org/10.1109/bicta.2010.5645093openalex-snapshot
Study on interaction between ampicillin antibody and detection interfering proteins by computer aided protein-protein docking for biosensor interesting
inferred← citeshttps://doi.org/10.1142/s0219720009004461openalex-snapshot
IN SILICO SCREENING OF PROTEIN–PROTEIN INTERACTIONS WITH ALL-TO-ALL RIGID DOCKING AND CLUSTERING: AN APPLICATION TO PATHWAY ANALYSIS
inferred← citeshttps://doi.org/10.1155/2013/983829openalex-snapshot
Epitope Mapping of Metuximab on CD147 Using Phage Display and Molecular Docking
inferred← citeshttps://doi.org/10.1186/1471-2105-13-7openalex-snapshot
Protein docking prediction using predicted protein-protein interface
inferred← citeshttps://doi.org/10.1186/s12859-017-1628-6openalex-snapshot
AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
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/10.13021/mars/6871openalex-snapshot
Application of a Topological Descriptor for Protein Interface Identification and Protein Binding Prediction
inferred← citeshttps://doi.org/10.1371/journal.pone.0007028openalex-snapshot
Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding
inferred← citeshttps://doi.org/10.1371/journal.pone.0017695openalex-snapshot
CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
inferred← citeshttps://doi.org/10.1371/journal.pone.0022477openalex-snapshot
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
inferred← citeshttps://doi.org/10.1371/journal.pone.0024657openalex-snapshot
Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library
inferred← citeshttps://doi.org/10.1371/journal.pone.0065011openalex-snapshot
Rice Mitogen Activated Protein Kinase Kinase and Mitogen Activated Protein Kinase Interaction Network Revealed by In-Silico Docking and Yeast Two-Hybrid Approaches
inferred← citeshttps://doi.org/10.1371/journal.pone.0072096openalex-snapshot
Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock
inferred← citeshttps://doi.org/10.1529/biophysj.108.130542openalex-snapshot
Conformation and Free Energy Analyses of the Complex of Calcium-Bound Calmodulin and the Fas Death Domain
inferred← citeshttps://doi.org/10.2147/aabc.s6347openalex-snapshot
Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction
inferred← citeshttps://doi.org/10.3109/10799893.2013.868903openalex-snapshot
Macromolecular structure and interaction studies of SigF and Usfx inMycobacterium tuberculosis
inferred← citeshttps://doi.org/10.3390/biology14070742openalex-snapshot
A TRIM Family-Based Strategy for TRIMCIV Target Prediction in a Pan-Cancer Context with Multi-Omics Data and Protein Docking Integration
inferred← citeshttps://doi.org/10.3390/ijms12010226openalex-snapshot
Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin
inferred← citeshttps://doi.org/10.3390/ijms20102568openalex-snapshot
Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch001openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch030openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.6026/97320630006035openalex-snapshot
Antigen-Antibody docking reveals the molecular basis for cross-reactivity of the 1918 and 2009 Influenza A/H1N1 pandemic viruses
inferred← citeshttps://doi.org/10.6026/97320630006266openalex-snapshot
Molecular basis of antigenic drift in Influenza A/H3N2 strains (1968-2007) in the light of antigen-antibody interactions
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.