Research graph
References from Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/nature14539
10.1038/nature14539 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
Deep learning in bioinformatics
2017 · External reference
10.1371/journal.pcbi.1008543
10.1371/journal.pcbi.1008543 · External reference
MutaBind2: predicting the impacts of single and multiple mutations on protein-protein interactions
10.1016/j.isci.2020.100939 · 2020 · External reference
10.1093/nar/gkw374
10.1093/nar/gkw374 · External reference
PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions
10.1038/s42003-021-02826-3 · 2021 · External reference
10.1021/ct401022c
10.1021/ct401022c · External reference
PremPRI: predicting the effects of missense mutations on protein-RNA interactions
2020 · External reference
10.1371/journal.pcbi.1006615
10.1371/journal.pcbi.1006615 · External reference
Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset
10.1093/bib/bbab555 · 2022 · External reference
Bioinformatics toolbox for exploring target mutation-induced drug resistance
10.1093/bib/bbad033 · 2023 · External reference
Recent advances in user-friendly computational tools to engineer protein function
10.1093/bib/bbaa150 · 2021 · External reference
10.1016/j.sbi.2021.11.001
10.1016/j.sbi.2021.11.001 · External reference
An antisymmetric neural network to predict free energy changes in protein variants
10.1088/1361-6463/abedfb · 2021 · External reference
Discrimination and prediction of protein-protein binding affinity using deep learning approach
2018 · External reference
SeBPPI: a sequence-based protein–protein binding predictor
10.1142/s2737416522500314 · 2022 · External reference
Principles of protein-protein interactions
10.1073/pnas.93.1.13 · 1996 · External reference
10.1016/j.sbi.2013.08.002
10.1016/j.sbi.2013.08.002 · External reference
10.1002/jcp.20356
10.1002/jcp.20356 · External reference
Exploring protein-protein interactions as drug targets for anti-cancer therapy with in silico workflows
10.1007/978-1-4939-7201-2_15 · 2017 · External reference
10.1038/npp.2008.151
10.1038/npp.2008.151 · External reference
10.1093/abt/tbab003
10.1093/abt/tbab003 · External reference
10.1098/rsif.2012.0835
10.1098/rsif.2012.0835 · External reference
10.2174/1568009618666180803104631
10.2174/1568009618666180803104631 · External reference
Analysis of biomolecules using surface plasmons
10.1007/978-1-59745-483-4_14 · 2009 · External reference
10.1016/s1074-5521(96)90063-0
10.1016/s1074-5521(96)90063-0 · External reference
Protein-binding dynamics imaged in a living cell
10.1073/pnas.1112171109 · 2012 · External reference
10.1038/nrm1859
10.1038/nrm1859 · External reference
10.1126/science.1202617
10.1126/science.1202617 · External reference
Computational prediction of protein–protein binding affinities
2019 · External reference
On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities
10.1073/pnas.1114017109 · 2012 · External reference
Rapid, accurate, precise, and reliable relative free energy prediction using ensemble based thermodynamic integration
10.1021/acs.jctc.6b00979 · 2017 · External reference
10.1002/jcc.21372
10.1002/jcc.21372 · External reference
Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation
10.1021/acsomega.1c07037 · 2022 · External reference
Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction
10.1002/pro.257 · 2009 · External reference
10.1021/jm049314d
10.1021/jm049314d · External reference
PPI-Affinity: a web tool for the prediction and optimization of protein-peptide and protein-protein binding affinity
10.1021/acs.jproteome.2c00020 · 2022 · External reference
Protein-protein interactions: scoring schemes and binding affinity
10.1016/j.sbi.2016.10.016 · 2017 · External reference
10.1093/bioinformatics/btr513
10.1093/bioinformatics/btr513 · External reference
Prediction of protein-protein binding free energies
10.1002/pro.2027 · 2012 · External reference
Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding
10.1016/j.bpj.2015.01.001 · 2015 · External reference
ISLAND: in-silico proteins binding affinity prediction using sequence information
10.1186/s13040-020-00231-w · 2020 · External reference
10.7554/elife.07454
10.7554/elife.07454 · External reference
10.1093/bioinformatics/btw514
10.1093/bioinformatics/btw514 · External reference
Protein-protein binding affinity prediction from amino acid sequence
10.1093/bioinformatics/btu580 · 2014 · External reference
10.1126/science.ade2574
10.1126/science.ade2574 · External reference
Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
10.1016/j.jmb.2015.07.016 · 2015 · External reference
10.1093/bioinformatics/bty635
10.1093/bioinformatics/bty635 · External reference
PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics
10.1093/bioinformatics/btx312 · 2017 · External reference
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
10.1021/jm030580l · 2004 · External reference
Comparative protein structure modeling using MODELLER
10.1002/cpbi.3 · 2016 · External reference
10.1093/nar/28.1.235
10.1093/nar/28.1.235 · External reference
10.1016/0263-7855(96)00018-5
10.1016/0263-7855(96)00018-5 · External reference
10.1021/jp973084f
10.1021/jp973084f · External reference
10.1002/jcc.20289
10.1002/jcc.20289 · External reference
10.1038/nbt.3988
10.1038/nbt.3988 · External reference
10.1093/nar/gki524
10.1093/nar/gki524 · External reference
Unresolved reference
External reference
10.1002/jcc.540040211
10.1002/jcc.540040211 · External reference
10.1093/nar/gkq1105
10.1093/nar/gkq1105 · External reference
10.1002/bip.360221211
10.1002/bip.360221211 · External reference
10.1371/journal.pone.0046688
10.1371/journal.pone.0046688 · External reference
SOLart: a structure-based method to predict protein solubility and aggregation
10.1093/bioinformatics/btz773 · 2020 · External reference
10.1126/science.4023714
10.1126/science.4023714 · External reference
10.1093/nar/gkm998
10.1093/nar/gkm998 · External reference
Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces
10.1093/bioinformatics/18.4.608 · 2002 · External reference
10.1016/j.bpj.2018.07.035
10.1016/j.bpj.2018.07.035 · External reference
10.1007/s00894-009-0541-y
10.1007/s00894-009-0541-y · External reference
10.1002/pro.580
10.1002/pro.580 · External reference
10.1002/prot.24235
10.1002/prot.24235 · External reference
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker
10.1093/nar/gkab1050 · 2022 · External reference
SAbDab: the structural antibody database
10.1093/nar/gkt1043 · 2014 · External reference
PDBe: Protein Data Bank in Europe
10.1093/nar/gkt1180 · 2014 · External reference
10.1016/s0022-2836(02)00442-4
10.1016/s0022-2836(02)00442-4 · External reference
10.1371/journal.pone.0020161
10.1371/journal.pone.0020161 · External reference
Unresolved reference
External reference
10.1002/prot.22921
10.1002/prot.22921 · External reference
CCharPPI web server: computational characterization of protein-protein interactions from structure
10.1093/bioinformatics/btu594 · 2015 · External reference
ZRANK: reranking protein docking predictions with an optimized energy function
10.1002/prot.21373 · 2007 · External reference
10.1002/prot.21920
10.1002/prot.21920 · External reference
10.1093/bioinformatics/btq007
10.1093/bioinformatics/btq007 · External reference
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
10.1002/prot.21419 · 2007 · External reference
10.1002/prot.21495
10.1002/prot.21495 · External reference
Improving ranking of models for protein complexes with side chain modeling and atomic potentials
10.1002/prot.24214 · 2013 · External reference
10.1002/prot.22550
10.1002/prot.22550 · External reference
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking
10.1021/ci100353e · 2011 · External reference
A Monte Carlo evaluation of tests for comparing dependent correlations
10.1080/00221300309601282 · 2003 · External reference
Comparing the areas under 2 or more correlated receiver operating characteristic curves - a nonparametric approach
10.2307/2531595 · 1988 · External reference
10.1371/journal.pone.0121945
10.1371/journal.pone.0121945 · External reference
Unresolved reference
External reference
Evaluation of alphafold-multimer prediction on multi-chain protein complexes
2023 · External reference
10.1038/nprot.2016.169
10.1038/nprot.2016.169 · External reference
Binding affinity via docking: fact and fiction
10.3390/molecules23081899 · 2018 · External reference