On the public citation graph

Assessing the energy landscape of CAPRI targets by FunHunt

https://doi.org/10.1002/prot.21736
0 signed · 60 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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.20084openalex-snapshot
UCSF Chimera—A visualization system for exploratory research and analysis
inferredcites →https://doi.org/10.1002/prot.10115openalex-snapshot
Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
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.10393openalex-snapshot
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
inferredcites →https://doi.org/10.1002/prot.10395openalex-snapshot
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
inferredcites →https://doi.org/10.1002/prot.20305openalex-snapshot
The ConSurf‐HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
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.20556openalex-snapshot
Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility
inferredcites →https://doi.org/10.1002/prot.20575openalex-snapshot
Improving CAPRI predictions: Optimized desolvation for rigid‐body docking
inferredcites →https://doi.org/10.1002/prot.20842openalex-snapshot
WHISCY: What information does surface conservation yield? Application to data‐driven docking
inferredcites →https://doi.org/10.1002/prot.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1007/bf00994018openalex-snapshot
Support-Vector Networks
inferredcites →https://doi.org/10.1016/j.jmb.2003.10.069openalex-snapshot
Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes
inferredcites →https://doi.org/10.1016/j.jmb.2005.01.058openalex-snapshot
The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking
inferredcites →https://doi.org/10.1016/j.jmb.2005.09.028openalex-snapshot
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
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.str.2007.11.013openalex-snapshot
Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels
inferredcites →https://doi.org/10.1016/j.tibtech.2004.01.006openalex-snapshot
Protein–protein docking: is the glass half-full or half-empty?
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/s0076-6879(04)83004-0openalex-snapshot
Protein Structure Prediction Using Rosetta
inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1017/s0031182001008460openalex-snapshot
Anti-SAG1 peptide antibodies inhibit the penetration ofToxoplasma gondiitachyzoites into enterocyte cell lines
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/ja070153nopenalex-snapshot
Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein
inferredcites →https://doi.org/10.1023/a:1012487302797openalex-snapshot
Gene Selection for Cancer Classification using Support Vector Machines
inferredcites →https://doi.org/10.1038/nature02582openalex-snapshot
Structural basis of protein phosphatase 1 regulation
inferredcites →https://doi.org/10.1038/sj.emboj.7600162openalex-snapshot
Structural inhibition of the colicin D tRNase by the tRNA‐mimicking immunity protein
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/10.1073/pnas.0400014101openalex-snapshot
Insight into the PrP C → PrP Sc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants
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/10.1073/pnas.1936124100openalex-snapshot
Cellulosome assembly revealed by the crystal structure of the cohesin–dockerin complex
inferredcites →https://doi.org/10.1074/jbc.m404212200openalex-snapshot
Structural Basis for Inhibition of Aspergillus niger Xylanase by Triticum aestivum Xylanase Inhibitor-I
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/btl654openalex-snapshot
A new protein–protein docking scoring function based on interface residue properties
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gki481openalex-snapshot
PatchDock and SymmDock: servers for rigid and symmetric docking
inferredcites →https://doi.org/10.1110/ps.041081905openalex-snapshot
Assessing predictions of protein–protein interaction: The CAPRI experiment
inferredcites →https://doi.org/10.1110/ps.041222905openalex-snapshot
Improved side‐chain modeling for protein–protein docking
inferredcites →https://doi.org/10.1126/science.1112160openalex-snapshot
Progress in Modeling of Protein Structures and Interactions
inferredcites →https://doi.org/10.1529/biophysj.104.058768openalex-snapshot
Optimal Clustering for Detecting Near-Native Conformations in Protein Docking
inferredcites →https://doi.org/10.5555/299094openalex-snapshot
Advances in kernel methods: support vector learning

What points at this work

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

inferred← citeshttps://doi.org/10.1002/prot.24369openalex-snapshot
A Markov‐chain model description of binding funnels to enhance the ranking of docked solutions
inferred← citeshttps://doi.org/10.1002/prot.24423openalex-snapshot
Using a consensus approach based on the conservation of inter‐residue contacts to rank CAPRI models
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.2009.12.053openalex-snapshot
Rapid Structural Characterization of Human Antibody–Antigen Complexes through Experimentally Validated Computational Docking
inferred← citeshttps://doi.org/10.1016/j.str.2007.11.013openalex-snapshot
Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels
inferred← citeshttps://doi.org/10.1038/s42003-023-04657-wopenalex-snapshot
Targeting Ras-binding domain of ELMO1 by computational nanobody design
inferred← citeshttps://doi.org/10.1039/c005060copenalex-snapshot
Protein–protein docking tested in blind predictions: the CAPRI experiment
inferred← citeshttps://doi.org/10.1042/bst0361418openalex-snapshot
FunHunt: model selection based on energy landscape characteristics
inferred← citeshttps://doi.org/10.1093/nar/gkn216openalex-snapshot
The RosettaDock server for local protein-protein docking
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/10.13021/mars/6871openalex-snapshot
Application of a Topological Descriptor for Protein Interface Identification and Protein Binding Prediction
inferred← citeshttps://doi.org/10.1371/journal.pone.0050769openalex-snapshot
Using RosettaLigand for Small Molecule Docking into Comparative Models
inferred← citeshttps://doi.org/10.1371/journal.pone.0063906openalex-snapshot
Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)
inferred← citeshttps://doi.org/10.1529/biophysj.108.132977openalex-snapshot
Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions
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/10.6564/jkmrs.2011.15.1.080openalex-snapshot
3D Structure of STAM1 UIM-ubiquitin Complex Using RosettaDock
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.