On the public citation graph
On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking
0 signed · 96 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.
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known work and none has been retracted — and get a dated CiteStamped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.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990515)35:3<364::aid-prot11>3.0.co;2-4openalex-snapshot
Use of pair potentials across protein interfaces in screening predicted docked complexes
inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000501)39:2<178::aid-prot8>3.0.co;2-6openalex-snapshot
Protein docking using spherical polar Fourier correlations
inferredcites →https://doi.org/10.1002/0471140864.ps0209s50openalex-snapshot
Comparative Protein Structure Modeling Using MODELLER
inferredcites →https://doi.org/10.1002/prot.10222openalex-snapshot
MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading
inferredcites →https://doi.org/10.1002/prot.10383openalex-snapshot
ICM‐DISCO docking by global energy optimization with fully flexible side‐chains
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.10394openalex-snapshot
Successful discrimination of protein interactions
inferredcites →https://doi.org/10.1002/prot.20285openalex-snapshot
Optimal docking area: A new method for predicting protein–protein interaction sites
inferredcites →https://doi.org/10.1002/prot.20554openalex-snapshot
Classification of protein complexes based on docking difficulty
inferredcites →https://doi.org/10.1002/prot.20566openalex-snapshot
ATTRACT: Protein–protein docking in CAPRI using a reduced protein model
inferredcites →https://doi.org/10.1002/prot.21117openalex-snapshot
PIPER: An FFT‐based protein docking program with pairwise potentials
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.21419openalex-snapshot
pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21442openalex-snapshot
Identification of near‐native structures by clustering protein docking conformations
inferredcites →https://doi.org/10.1002/prot.21502openalex-snapshot
Integrating statistical pair potentials into protein complex prediction
inferredcites →https://doi.org/10.1002/prot.21698openalex-snapshot
Implicit flexibility in protein docking: Cross‐docking and local refinement
inferredcites →https://doi.org/10.1002/prot.22106openalex-snapshot
Protein–protein docking benchmark version 3.0
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.22830openalex-snapshot
Protein–protein docking benchmark version 4.0
inferredcites →https://doi.org/10.1002/prot.22844openalex-snapshot
How different from random are docking predictions when ranked by scoring functions?
inferredcites →https://doi.org/10.1006/jmbi.1996.0868openalex-snapshot
Novel knowledge-based mean force potential at atomic level
inferredcites →https://doi.org/10.1006/jmbi.1997.1203openalex-snapshot
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1016/0022-2836(78)90302-9openalex-snapshot
Computer analysis of protein-protein interaction
inferredcites →https://doi.org/10.1016/j.jmb.2008.04.071openalex-snapshot
Architectures and Functional Coverage of Protein–Protein Interfaces
inferredcites →https://doi.org/10.1016/j.sbi.2006.05.003openalex-snapshot
Target selection for complex structural genomics
inferredcites →https://doi.org/10.1016/j.sbi.2009.02.008openalex-snapshot
Convergence and combination of methods in protein–protein docking
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/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1021/pr070426dopenalex-snapshot
Biological Pathways Contributing to Organ-Specific Phenotype of Brain Metastatic Cells
inferredcites →https://doi.org/10.1021/pr800137wopenalex-snapshot
Functional Clustering of Metastasis Proteins Describes Plastic Adaptation Resources of Breast-Cancer Cells to New Microenvironments
inferredcites →https://doi.org/10.1038/nature04532openalex-snapshot
Proteome survey reveals modularity of the yeast cell machinery
inferredcites →https://doi.org/10.1038/nature06404openalex-snapshot
Determining the architectures of macromolecular assemblies
inferredcites →https://doi.org/10.1063/1.1824012openalex-snapshot
How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?
inferredcites →https://doi.org/10.1073/pnas.0802496105openalex-snapshot
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–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/10.1093/bioinformatics/19.1.161openalex-snapshot
InterPreTS: protein Interaction Prediction through Tertiary Structure
inferredcites →https://doi.org/10.1093/bioinformatics/btg371openalex-snapshot
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
inferredcites →https://doi.org/10.1093/bioinformatics/btp238openalex-snapshot
ModLink+: improving fold recognition by using protein–protein interactions
inferredcites →https://doi.org/10.1093/bioinformatics/btp447openalex-snapshot
FRODOCK: a new approach for fast rotational protein–protein docking
inferredcites →https://doi.org/10.1093/nar/gkn332openalex-snapshot
DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions
inferredcites →https://doi.org/10.1093/nar/gkn573openalex-snapshot
Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
inferredcites →https://doi.org/10.1093/nar/gkn690openalex-snapshot
3did Update: domain-domain and peptide-mediated interactions of known 3D structure
inferredcites →https://doi.org/10.1093/nar/gkp289openalex-snapshot
Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface
inferredcites →https://doi.org/10.1093/nar/gkp944openalex-snapshot
GWIDD: Genome-wide protein docking database
inferredcites →https://doi.org/10.1110/ps.062416606openalex-snapshot
Statistical potential for assessment and prediction of protein structures
inferredcites →https://doi.org/10.1126/science.1092645openalex-snapshot
Structure-Based Assembly of Protein Complexes in Yeast
inferredcites →https://doi.org/10.1186/1471-2105-9-172openalex-snapshot
Predicting cancer involvement of genes from heterogeneous data
inferredcites →https://doi.org/10.1186/1472-6807-9-71openalex-snapshot
Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations
inferredcites →https://doi.org/10.1371/journal.pcbi.0030178openalex-snapshot
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
inferredcites →https://doi.org/10.1371/journal.pcbi.1000490openalex-snapshot
Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments
inferredcites →https://doi.org/10.1371/journal.pcbi.1000601openalex-snapshot
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
inferredcites →https://doi.org/10.1371/journal.pcbi.1000727openalex-snapshot
Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling
inferredcites →https://doi.org/10.1529/biophysj.107.114280openalex-snapshot
M-TASSER: An Algorithm for Protein Quaternary Structure Prediction
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527830503.ch4openalex-snapshot
Computational Protein–Protein Docking
inferred← citeshttps://doi.org/10.1002/jmr.2555openalex-snapshot
Optimization of protein–protein docking for predicting Fc–protein interactions
inferred← citeshttps://doi.org/10.1002/minf.201200005openalex-snapshot
Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details
inferred← citeshttps://doi.org/10.1002/pro.3930openalex-snapshot
Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions
inferred← citeshttps://doi.org/10.1002/prot.24022openalex-snapshot
Fast and accurate modeling of protein–protein interactions by combining template‐interface‐based docking with flexible refinement
inferred← citeshttps://doi.org/10.1002/prot.25218openalex-snapshot
A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison
inferred← citeshttps://doi.org/10.1007/978-1-0716-1767-0_16openalex-snapshot
Prediction of Protein–Protein Binding Affinities from Unbound Protein Structures
inferred← citeshttps://doi.org/10.1007/978-1-0716-2617-7_4openalex-snapshot
Modeling Protein Complexes and Molecular Assemblies Using Computational Methods
inferred← citeshttps://doi.org/10.1016/b978-0-12-800168-4.00004-4openalex-snapshot
On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions
inferred← citeshttps://doi.org/10.1016/j.carres.2020.108180openalex-snapshot
Comprehensive analysis of carbohydrate-protein recognition in the Protein Data Bank
inferred← citeshttps://doi.org/10.1016/j.foodhyd.2026.112987openalex-snapshot
The “skeleton effect” of Ovomucin precisely regulates the gelation behavior of major egg white proteins: Differentiated thermodynamic driving mechanisms and the roles of key glycopeptide regions
inferred← citeshttps://doi.org/10.1016/j.isci.2024.109584openalex-snapshot
Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation
inferred← citeshttps://doi.org/10.1016/j.jmb.2020.09.015openalex-snapshot
Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.04.001openalex-snapshot
Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein–protein docking results
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2014.07.004openalex-snapshot
An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles
inferred← citeshttps://doi.org/10.1021/ct400295zopenalex-snapshot
Intermolecular Contact Potentials for Protein–Protein Interactions Extracted from Binding Free Energy Changes upon Mutation
inferred← citeshttps://doi.org/10.1038/s41598-020-80900-2openalex-snapshot
Classification and prediction of protein–protein interaction interface using machine learning algorithm
inferred← citeshttps://doi.org/10.1038/s42256-025-01136-1openalex-snapshot
An interaction-derived graph learning framework for scoring protein–peptide complexes
inferred← citeshttps://doi.org/10.1042/bst20150001openalex-snapshot
InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu594openalex-snapshot
CCharPPI web server: computational characterization of protein–protein interactions from structure
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx584openalex-snapshot
Protein–protein interaction specificity is captured by contact preferences and interface composition
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx616openalex-snapshot
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures
inferred← citeshttps://doi.org/10.1093/nargab/lqaa046openalex-snapshot
On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF
inferred← citeshttps://doi.org/10.1093/nargab/lqae068openalex-snapshot
Structure-based learning to predict and model protein–DNA interactions and transcription-factor co-operativity in cis-regulatory elements
inferred← citeshttps://doi.org/10.1101/2022.04.17.488557openalex-snapshot
Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis -regulatory elements
inferred← citeshttps://doi.org/10.1111/cbdd.12076openalex-snapshot
Advances in the Prediction of Protein–Peptide Binding Affinities: Implications for Peptide‐Based Drug Discovery
inferred← citeshttps://doi.org/10.1186/1471-2105-14-286openalex-snapshot
The scoring of poses in protein-protein docking: current capabilities and future directions
inferred← citeshttps://doi.org/10.1186/s12859-020-03770-5openalex-snapshot
SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
inferred← citeshttps://doi.org/10.1371/journal.pone.0118107openalex-snapshot
VORFFIP-Driven Dock: V-D2OCK, a Fast and Accurate Protein Docking Strategy
inferred← citeshttps://doi.org/10.3389/fmolb.2020.559005openalex-snapshot
Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses
inferred← citeshttps://doi.org/10.3390/ijms20174168openalex-snapshot
Wnt Binding Affinity Prediction for Putative Frizzled-Type Cysteine-Rich Domains
inferred← citeshttps://doi.org/10.3390/ijms242015239openalex-snapshot
The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins
inferred← citeshttps://doi.org/10.4155/fmc.12.99openalex-snapshot
Recent Work In The Development And Application Of Protein–Peptide Docking
inferred← citeshttps://doi.org/10.5772/37856openalex-snapshot
Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence
inferred← citeshttps://doi.org/10.6084/m9.figshare.13534444openalex-snapshot
Additional file 13 of SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.13534447openalex-snapshot
Additional file 14 of SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.13534450openalex-snapshot
Additional file 15 of SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.13534453openalex-snapshot
Additional file 16 of SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
inferred← citeshttps://doi.org/10.6084/m9.figshare.13534459openalex-snapshot
Additional file 1 of SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
inferred← citeshttps://doi.org/10.64898/2026.02.18.701901openalex-snapshot
ModCRElib: A standalone package to model cis -regulatory elements
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.