Research graph
References from Protein interactions with small molecules, peptides and proteins share residue cluster classes. Local targets link to admitted publications; unresolved targets remain external evidence.
Natively unfolded proteins: a point where biology waits for physics
10.1110/ps.4210102 · 2002 · External reference
The metastable states of proteins
10.1002/pro.3859 · 2020 · External reference
Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
10.1146/annurev-biophys-102622-084607 · 2023 · External reference
Improved prediction of protein‒protein interactions using AlphaFold2
10.1038/s41467-022-28865-w · 2022 · External reference
Progress at protein structure prediction, as seen in CASP15
10.1016/j.sbi.2023.102594 · 2023 · External reference
The iPPI-DB initiative: a community-centered database of protein‒protein interaction modulators
10.1093/bioinformatics/btaa1091 · 2021 · External reference
Generating potential protein‒protein interaction inhibitor molecules based on physicochemical properties
10.3390/molecules28155652 · 2023 · External reference
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation
10.1038/s44320-023-00005-6 · 2024 · External reference
Protein-peptide docking: opportunities and challenges
10.1016/j.drudis.2018.05.006 · 2018 · External reference
Protein interaction interface region prediction by geometric deep learning
10.1093/bioinformatics/btab154 · 2021 · External reference
10.1016/j.csbj.2022.08.070 · 2022 · Admitted local publication
Protein‒Protein interactions efficiently modeled by residue cluster classes
10.3390/ijms21134787 · 2020 · External reference
PepBDB: a comprehensive structural database of biological peptide-protein interactions
10.1093/bioinformatics/bty579 · 2019 · External reference
Negatome 2.0: a database of noninteracting proteins derived by literature mining, manual annotation and protein structure analysis
10.1093/nar/gkt1079 · 2014 · External reference
InterPepRank: assessment of docked peptide conformations by a deep graph network
10.3389/fbinf.2021.763102 · 2021 · External reference
3did: a catalog of domain-based interactions of known three-dimensional structure
10.1093/nar/gkt887 · 2014 · External reference
The protein-small-molecule database, a nonredundant structural resource for the analysis of protein‒ligand binding
10.1093/bioinformatics/btp035 · 2009 · External reference
Machine learnable fold space representation based on residue cluster classes
10.1016/j.compbiolchem.2015.07.010 · 2015 · External reference
Residue cluster classes: a unified protein representation for efficient structural and functional classification
10.3390/e22040472 · 2020 · External reference
AutoWEKA 2.0: automatic model selection and hyperparameter optimization in WEKA
2017 · External reference
Unresolved reference
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Unresolved reference
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LIBSVM: a library for support vector machines
10.1145/1961189.1961199 · 2011 · External reference
Prediction of protein function using protein‒protein interaction data
10.1089/106652703322756168 · 2003 · External reference
Mining functional gene modules by multiview NMF of phenome-genome association
10.1186/s12864-024-11120-5 · 2025 · External reference
Protein‒protein docking using region-based 3D Zernike descriptors
10.1186/1471-2105-10-407 · 2009 · External reference
PL-PatchSurfer2: improved local surface matching-based virtual screening method that is tolerant to target and ligand structure variation
10.1021/acs.jcim.6b00163 · 2016 · External reference
Machine learning advances in predicting Peptide/Protein‒Protein interactions based on sequence information for lead peptides discovery
10.1002/adbi.202200232 · 2023 · External reference
10.1039/d3cb00208j
10.1039/d3cb00208j · External reference
Recent advances in the development of protein‒protein interactions modulators: mechanisms and clinical trials
10.1038/s41392-020-00315-3 · 2020 · External reference
Developing small-molecule inhibitors of protein‒protein interactions involved in viral entry as potential antivirals for COVID-19
10.3389/fddsv.2022.898035 · 2022 · External reference
Residue coordination in proteins conforms to the closest packing of spheres
10.1016/s0032-3861(01)00427-x · 2002 · External reference
Saturation mutagenesis of the Transmembrane Region of HokC in Escherichia coli reveals its high tolerance to mutations
10.3390/ijms221910359 · 2021 · External reference
Identification of small-molecule protein‒protein interaction inhibitors for NKG2D
10.1073/pnas.2216342120 · 2023 · External reference
The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme
10.1073/pnas.96.18.10118 · 1999 · External reference
Role of distal sites in enzyme engineering
10.1016/j.biotechadv.2023.108094 · 2023 · External reference
