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References from Protein–protein interaction prediction with deep learning: A comprehensive review. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
External reference
Probselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection
10.1093/bioinformatics/btaa806 · 2020 · External reference
Protein interactions: integration leads to belief
10.1016/j.tibs.2008.04.002 · 2008 · External reference
10.1371/journal.pcbi.1000807
10.1371/journal.pcbi.1000807 · External reference
Protein interactions: is seeing believing?
10.1016/j.tibs.2007.09.006 · 2007 · External reference
Protein-protein interaction interface residue pair prediction based on deep learning architecture
10.1109/tcbb.2017.2706682 · 2017 · External reference
10.1016/j.csbj.2020.02.008 · Admitted local publication
Recent advances in the development of protein–protein interactions modulators: mechanisms and clinical trials
2020 · External reference
Paying attention: Using a siamese pyramid network for the prediction of protein-protein interactions with folding and self-binding primary sequences
2021 · External reference
Deep graph embedding for prioritizing synergistic anticancer drug combinations, Computational and Structural
2020 · External reference
Deep learning in protein structural modeling and design
10.1016/j.patter.2020.100142 · 2020 · External reference
Principles of protein-protein interactions
10.1073/pnas.93.1.13 · 1996 · External reference
Prediction of protein interaction sites from sequence profile and residue neighbor list, Proteins: Structure
10.1002/prot.1099 · 2001 · External reference
10.1007/s12033-007-0069-2
10.1007/s12033-007-0069-2 · External reference
10.1186/1471-2105-15-s15-s9
10.1186/1471-2105-15-s15-s9 · External reference
10.1016/j.sbi.2015.12.004
10.1016/j.sbi.2015.12.004 · External reference
10.1088/1742-6596/1937/1/012011
10.1088/1742-6596/1937/1/012011 · External reference
Sequence-based prediction of protein protein interaction using a deep-learning algorithm
2017 · External reference
A survey of current trends in computational predictions of protein-protein interactions
10.1007/s11704-019-8232-z · 2020 · External reference
10.1128/mr.59.1.94-123.1995
10.1128/mr.59.1.94-123.1995 · External reference
10.1021/acs.jproteome.0c00359
10.1021/acs.jproteome.0c00359 · External reference
Functional identification of ’hypothetical protein-structures with unknown function
10.1080/07391102.2022.2085806 · 2022 · External reference
10.1126/science.1087361
10.1126/science.1087361 · External reference
10.3390/molecules23040823
10.3390/molecules23040823 · External reference
10.1038/82360
10.1038/82360 · External reference
10.1073/pnas.97.3.1143
10.1073/pnas.97.3.1143 · External reference
10.1038/415141a
10.1038/415141a · External reference
10.1038/415180a
10.1038/415180a · External reference
10.1038/35015709
10.1038/35015709 · External reference
Novel approaches to map protein interactions
10.1016/s0958-1669(02)00005-8 · 2003 · External reference
10.1093/bib/bbz163
10.1093/bib/bbz163 · External reference
Desorption electrospray ionization mass spectrometry imaging of proteins directly from biological tissue sections
10.1021/acs.analchem.8b00967 · 2018 · External reference
10.1126/science.289.5485.1760
10.1126/science.289.5485.1760 · External reference
A human cdna library for high-throughput protein expression screening
10.1006/geno.2000.6141 · 2000 · External reference
10.1016/s0166-6851(01)00366-8
10.1016/s0166-6851(01)00366-8 · External reference
The flexgene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era
10.1016/s0188-4409(02)00372-7 · 2002 · External reference
10.1677/jme.1.01693
10.1677/jme.1.01693 · External reference
10.1002/cmdc.201500495
10.1002/cmdc.201500495 · External reference
New methodologies for measuring protein interactions in vivo and in vitro
10.1016/j.sbi.2005.01.008 · 2005 · External reference
Protein-protein interaction detection: methods and analysis
2014 · External reference
Computational identification of protein-protein interactions in model plant proteomes
10.1038/s41598-019-45072-8 · 2019 · External reference
Unresolved reference
External reference
Molecular cell biology
2001 · External reference
Unresolved reference
External reference
10.1007/978-981-10-7455-4_7
10.1007/978-981-10-7455-4_7 · External reference
Respective roles of short-and long-range interactions in protein folding
10.1073/pnas.75.2.559 · 1978 · External reference
Importance of long-range interactions in protein folding
10.1016/s0301-4622(99)00010-1 · 1999 · External reference
10.1016/j.pbiomolbio.2017.09.018
10.1016/j.pbiomolbio.2017.09.018 · External reference
10.1023/a:1004981409616
10.1023/a:1004981409616 · External reference
Unresolved reference
External reference
10.1016/b978-0-12-374984-0.00051-6
10.1016/b978-0-12-374984-0.00051-6 · 2013 · External reference
Prediction of protein-protein interactions with local weight-sharing mechanism in deep learning
2020 · External reference
10.1016/0022-2836(82)90515-0
10.1016/0022-2836(82)90515-0 · External reference
Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks
10.1007/s008940100038 · 2001 · External reference
Molecular connectivity model for determination of isoelectric point of amino acids
10.1002/jps.2600810407 · 1992 · External reference
Amino acid size, charge, hydropathy indices and matrices for protein structure analysis
10.1186/1742-4682-3-15 · 2006 · External reference
Amino acid side chain parameters for correlation studies in biology and pharmacology
10.1111/j.1399-3011.1988.tb01261.x · 1988 · External reference
10.1126/science.273.5275.595
10.1126/science.273.5275.595 · External reference
10.1021/jz402762h
10.1021/jz402762h · External reference
Prediction of protein-protein interactions using stacked auto-encoder
2021 · External reference
On the evolution of the standard amino-acid alphabet
2006 · External reference
Synthesis and decoding of selenocysteine and human health
10.3325/cmj.2012.53.535 · 2012 · External reference
10.1074/jbc.m501458200
10.1074/jbc.m501458200 · External reference
How selenium has altered our understanding of the genetic code
10.1128/mcb.22.11.3565-3576.2002 · 2002 · External reference
Biosynthesis of selenocysteine, the 21st amino acid in the genetic code, and a novel pathway for cysteine biosynthesis
10.3945/an.110.000265 · 2011 · External reference
Nomenclature and symbolism for amino acids and peptides
10.1351/pac198456050595 · 1984 · External reference
Unresolved reference
2018 · External reference
Mobility shift-affinity capillary electrophoresis for investigation of protein-metal ion interactions: aspects of method development, validation and high throughput screening
2015 · External reference
An effective machine learning-based model for the prediction of protein–protein interaction sites in health systems
2022 · External reference
Unresolved reference
2019 · External reference
10.1146/annurev.biochem.77.032207.120833
10.1146/annurev.biochem.77.032207.120833 · External reference
Determination of hydroxyproline
10.1016/0009-8981(67)90167-2 · 1967 · External reference
Unresolved reference
External reference
10.1126/science.1089427
10.1126/science.1089427 · External reference
Structural characteristics of novel protein folds
10.1371/journal.pcbi.1000750 · 2010 · External reference
10.1126/science.1152692
10.1126/science.1152692 · External reference
10.1038/nature06879
10.1038/nature06879 · External reference
10.1016/j.str.2010.06.010
10.1016/j.str.2010.06.010 · External reference
10.1016/j.str.2016.02.013
10.1016/j.str.2016.02.013 · External reference
10.1038/nbt.2797
10.1038/nbt.2797 · External reference
10.1038/nature12966
10.1038/nature12966 · External reference
10.1038/nature12443
10.1038/nature12443 · External reference
10.1038/nchem.1856
10.1038/nchem.1856 · External reference
10.1126/science.1219364
10.1126/science.1219364 · External reference
10.1038/nature13404
10.1038/nature13404 · External reference
10.1126/science.aaa9897
10.1126/science.aaa9897 · External reference
10.1126/science.aaf8818
10.1126/science.aaf8818 · External reference
10.1007/978-1-4939-6637-0
10.1007/978-1-4939-6637-0 · 2017 · External reference
10.1021/ja107487b
10.1021/ja107487b · External reference
10.1126/science.1261172
10.1126/science.1261172 · External reference
10.1021/cb500759p
10.1021/cb500759p · External reference
10.1038/nature19946
10.1038/nature19946 · External reference
10.1016/j.sbi.2016.04.002
10.1016/j.sbi.2016.04.002 · External reference
10.1016/j.sbi.2016.06.013
10.1016/j.sbi.2016.06.013 · External reference
10.1016/j.sbi.2016.11.021
10.1016/j.sbi.2016.11.021 · External reference
10.1110/ps.9.4.812
10.1110/ps.9.4.812 · External reference
10.1146/annurev-biophys-083012-130315
10.1146/annurev-biophys-083012-130315 · External reference
10.1016/j.sbi.2007.03.006
10.1016/j.sbi.2007.03.006 · External reference
10.1016/j.str.2011.03.019
10.1016/j.str.2011.03.019 · External reference
10.1038/nature16191
10.1038/nature16191 · External reference
10.1038/nature19791
10.1038/nature19791 · External reference
10.1016/j.sbi.2016.05.007
10.1016/j.sbi.2016.05.007 · External reference
10.1002/pro.2892
10.1002/pro.2892 · External reference
Computational protein design with deep learning neural networks
2018 · External reference
10.1038/nature14539
10.1038/nature14539 · External reference
10.1093/nar/gkaa1100
10.1093/nar/gkaa1100 · External reference
Swiss-model: homology modelling of protein structures and complexes
10.1093/nar/gky427 · 2018 · External reference
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis
10.1093/nar/gkt1079 · 2014 · External reference
10.1093/nar/gkaa1074
10.1093/nar/gkaa1074 · External reference
Rcsb protein data bank: improved annotation, search and visualization of membrane protein structures archived in the pdb
10.1093/bioinformatics/btab813 · 2022 · External reference
10.1002/pro.3978
10.1002/pro.3978 · External reference
Dip, the database of interacting proteins: a research tool for studying cellular networks of protein interactions
10.1093/nar/30.1.303 · 2002 · External reference
Bind: the biomolecular interaction network database
10.1093/nar/gkg056 · 2003 · External reference
Using the mint database to search protein interactions
10.1002/cpbi.93 · 2020 · External reference
Human protein reference database–2009 update
10.1093/nar/gkn892 · 2009 · External reference
The mintact project–intact as a common curation platform for 11 molecular interaction databases
10.1093/nar/gkt1115 · 2014 · External reference
A survey on computational models for predicting protein–protein interactions
10.1093/bib/bbab036 · 2021 · External reference
10.1126/science.181.4096.223
10.1126/science.181.4096.223 · External reference
Production and characterization of antioxidative peptides during lactic fermentation of goat milk
10.1111/jfpp.15992 · 2021 · External reference
10.1007/978-3-030-02634-9_3
10.1007/978-3-030-02634-9_3 · External reference
10.1016/j.jmb.2020.11.003
10.1016/j.jmb.2020.11.003 · External reference
The scop database in 2020: expanded classification of representative family and superfamily domains of known protein structures
10.1093/nar/gkz1064 · 2020 · External reference
Conservation of gene order: a fingerprint of proteins that physically interact
10.1016/s0968-0004(98)01274-2 · 1998 · External reference
10.1093/jac/dkz400
10.1093/jac/dkz400 · External reference
Unresolved reference
External reference
Deep learning
10.1038/nature14539 · 2015 · External reference
10.1016/j.eswa.2020.113456
10.1016/j.eswa.2020.113456 · External reference
Learning long-term dependencies with gradient descent is difficult
10.1109/72.279181 · 1994 · External reference
Unresolved reference
2001 · External reference
Long short-term memory
10.1162/neco.1997.9.8.1735 · 1997 · External reference
Delay aware intelligent transient stability assessment system
10.1109/access.2017.2746093 · 2017 · External reference
Unresolved reference
2015 · External reference
10.1109/msp.2017.2693418
10.1109/msp.2017.2693418 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Graph convolutional networks: a comprehensive review
10.1186/s40649-019-0069-y · 2019 · External reference
The emerging field of signal processing on graphs: Extending high-dimensional data analysis to networks and other irregular domains
10.1109/msp.2012.2235192 · 2013 · External reference
Deep graph convolutional reinforcement learn-ing for financial portfolio management–deeppocket
10.1016/j.eswa.2021.115127 · 2021 · External reference
Unresolved reference
External reference
Unresolved reference
2011 · External reference
Unresolved reference
External reference
Graph convolutional networks: analysis, improvements and results
10.1007/s10489-021-02973-4 · 2022 · External reference
Unresolved reference
External reference
Long-term financial predictions based on feynman–dirac path integrals, deep bayesian networks and temporal generative adversarial networks
10.1016/j.mlwa.2022.100255 · 2022 · External reference
Unresolved reference
External reference
Unresolved reference
2014 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
A neural probabilistic language model
2003 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
2018 · External reference
Dagan: Deep de-aliasing generative adversarial networks for fast compressed sensing mri reconstruction
10.1109/tmi.2017.2785879 · 2017 · External reference
10.1016/j.neuroimage.2018.07.043
10.1016/j.neuroimage.2018.07.043 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Variational autoencoder based anomaly detection using reconstruction probability
2015 · External reference
Improved variational inference with inverse autoregressive flow
2016 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Computational analyses of high-throughput protein-protein interaction data
10.2174/1389203033487225 · 2003 · External reference
The methods employed in mass spectrometric analysis of posttranslational modifications (ptms) and protein–protein interactions (ppis)
10.1007/978-3-030-15950-4_10 · 2019 · External reference
Reliable identification of protein-protein interactions by crosslinking mass spectrometry
10.1038/s41467-021-23666-z · 2021 · External reference
Inferring protein-protein interaction networks from mass spectrometry-based proteomic approaches: a mini-review, Computational and Structural
2019 · External reference
Unresolved reference
External reference
10.1016/j.crci.2015.12.004
10.1016/j.crci.2015.12.004 · External reference
10.1016/j.sbi.2017.02.005
10.1016/j.sbi.2017.02.005 · External reference
10.1016/j.sbi.2022.102370
10.1016/j.sbi.2022.102370 · External reference
10.1126/science.1190239
10.1126/science.1190239 · External reference
10.1038/nbt.2214
10.1038/nbt.2214 · External reference
10.1038/nbt.3907
10.1038/nbt.3907 · External reference
Engineering a light-activated caspase-3 for precise ablation of neurons in vivo
10.1073/pnas.1705064114 · 2017 · External reference
Unresolved reference
2018 · External reference
A rosetta-based protein design protocol converging to natural sequences
10.1063/5.0039240 · 2021 · External reference
10.1038/nature11600
10.1038/nature11600 · External reference
10.1126/science.aan0693
10.1126/science.aan0693 · External reference
Unresolved reference
External reference
Unresolved reference
2019 · External reference
Unresolved reference
External reference
10.1016/j.cels.2019.03.006
10.1016/j.cels.2019.03.006 · External reference
10.1126/science.278.5335.82
10.1126/science.278.5335.82 · External reference
10.1110/ps.03190903
10.1110/ps.03190903 · External reference
10.1038/nature03990
10.1038/nature03990 · External reference
Computational methods for predicting protein-protein interactions using various protein features
10.1002/cpps.62 · 2018 · External reference
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets
10.1186/gb-2012-13-8-r76 · 2012 · External reference
Interpred: a pipeline to identify and model protein–protein interactions, Proteins: Structure
10.1002/prot.25280 · 2017 · External reference
Amalgamation of 3d structure and sequence information for protein–protein interaction prediction
2020 · External reference
10.1002/rcm.3737
10.1002/rcm.3737 · External reference
10.1016/j.jmb.2004.02.040
10.1016/j.jmb.2004.02.040 · External reference
10.1016/s0955-0674(03)00005-x
10.1016/s0955-0674(03)00005-x · External reference
10.1016/j.neucom.2019.05.013
10.1016/j.neucom.2019.05.013 · External reference
10.1134/s0006297909130112
10.1134/s0006297909130112 · External reference
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast
10.1186/1752-0509-6-128 · 2012 · External reference
10.1016/j.sbi.2013.08.002
10.1016/j.sbi.2013.08.002 · External reference
10.1093/bioinformatics/btx005
10.1093/bioinformatics/btx005 · External reference
Protein–protein interaction site prediction through combining local and global features with deep neural networks
10.1093/bioinformatics/btz699 · 2020 · External reference
10.1109/bibm52615.2021.9669435
10.1109/bibm52615.2021.9669435 · 2021 · External reference
10.1038/468851a
10.1038/468851a · External reference
Structure-aware protein–protein interaction site prediction using deep graph convolutional network
10.1093/bioinformatics/btab643 · 2022 · External reference
Club-martini: selecting favourable interactions amongst available candidates, a coarse-grained simulation approach to scoring docking decoys
10.1371/journal.pone.0155251 · 2016 · External reference
10.1016/j.gene.2008.06.014
10.1016/j.gene.2008.06.014 · External reference
10.3390/ijms21020467
10.3390/ijms21020467 · External reference
Delphi: accurate deep ensemble model for protein interaction sites prediction
10.1093/bioinformatics/btaa750 · 2021 · External reference
Effector molecules and regulatory proteins: Applications
10.1016/j.tibtech.2016.04.011 · 2016 · External reference
Deep learning for protein–protein interaction site prediction
2021 · External reference
10.1093/nar/gkx366
10.1093/nar/gkx366 · External reference
10.1016/j.tips.2012.03.006
10.1016/j.tips.2012.03.006 · External reference
An algorithm for predicting protein–protein interaction sites: abnormally exposed amino acid residues and secondary structure elements
10.1110/ps.051589106 · 2006 · External reference
Computational methods for protein-protein interaction and their application
10.2174/138920305774329313 · 2005 · External reference
10.1016/b978-0-323-90264-9.00009-x
10.1016/b978-0-323-90264-9.00009-x · External reference
Protein-protein docking: From interaction to interactome
10.1016/j.bpj.2014.08.033 · 2014 · External reference
Computational prediction of protein–protein binding affinities, Wiley Interdisciplinary Reviews: Computational Molecular
2020 · External reference
10.1007/978-3-662-00551-4_4
10.1007/978-3-662-00551-4_4 · External reference
10.1093/bioinformatics/btq007
10.1093/bioinformatics/btq007 · External reference
Unresolved reference
External reference
10.1093/bioinformatics/btu097
10.1093/bioinformatics/btu097 · External reference
Fiberdock: flexible induced-fit backbone refinement in molecular docking, Proteins: Structure
10.1002/prot.22668 · 2010 · External reference
Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
10.1016/s0022-2836(03)00670-3 · 2003 · External reference
10.1016/j.jmb.2007.07.050
10.1016/j.jmb.2007.07.050 · External reference
Unresolved reference
2011 · External reference
Megadock: an all-to-all protein-protein interaction prediction system using tertiary structure data
10.2174/09298665113209990050 · 2014 · External reference
10.1016/j.sbi.2013.11.005
10.1016/j.sbi.2013.11.005 · External reference
10.1126/science.278.5338.631
10.1126/science.278.5338.631 · External reference
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using prism
10.1038/nprot.2011.367 · 2011 · External reference
10.1110/ps.03484604
10.1110/ps.03484604 · External reference
10.1088/1478-3975/8/3/035006
10.1088/1478-3975/8/3/035006 · External reference
Templates are available to model nearly all complexes of structurally characterized proteins
10.1073/pnas.1200678109 · 2012 · External reference
Homcos: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures
10.1093/nar/gkn218 · 2008 · External reference
Spatial clustering of protein binding sites for template based protein docking
10.1093/bioinformatics/btr493 · 2011 · External reference
10.1093/bioinformatics/btz863
10.1093/bioinformatics/btz863 · External reference
Topmodel: template-based protein structure prediction at low sequence identity using top-down consensus and deep neural networks
10.1021/acs.jctc.9b00825 · 2020 · External reference
Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking, Proteins: Structure
10.1002/prot.25234 · 2017 · External reference
Template-based modeling of protein complexes using the ppi3d web server
10.1007/978-1-0716-0708-4_8 · 2020 · External reference
Template-based modeling and ab initio refinement of protein oligomer structures using galaxy in capri round 30, Proteins: Structure
10.1002/prot.25192 · 2017 · External reference
10.1016/j.ijbiomac.2008.05.004
10.1016/j.ijbiomac.2008.05.004 · External reference
Prism: protein interactions by structural matching
10.1093/nar/gki585 · 2005 · External reference
Predicting protein-protein interactions from primary protein sequences using a novel multi-scale local feature representation scheme and the random forest
10.1371/journal.pone.0125811 · 2015 · External reference
Using weighted sparse representation model combined with discrete cosine transformation to predict protein-protein interactions from protein sequence
10.1155/2015/902198 · 2015 · External reference
10.1016/j.neucom.2014.05.072
10.1016/j.neucom.2014.05.072 · External reference
Intpred: a structure-based predictor of protein–protein interaction sites
10.1093/bioinformatics/btx585 · 2018 · External reference
Unresolved reference
External reference
New graph distance for deformable 3d objects recognition based on triangle-stars decomposition
10.1016/j.patcog.2019.01.040 · 2019 · External reference
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map
10.1186/s13321-021-00488-1 · 2021 · External reference
Imputing single-cell rna-seq data by combining graph convolution and autoencoder neural networks
10.1016/j.isci.2021.102393 · 2021 · External reference
10.24963/ijcai.2020/392
10.24963/ijcai.2020/392 · External reference
Combining sequence and network information to enhance protein–protein interaction prediction
2020 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Pier: protein interface recognition for structural proteomics, Proteins: Structure
10.1002/prot.21233 · 2007 · External reference
Protein binding site prediction using an empirical scoring function
10.1093/nar/gkl454 · 2006 · External reference
meta-ppisp: a meta web server for protein-protein interaction site prediction
10.1093/bioinformatics/btm434 · 2007 · External reference
Prediction-based fingerprints of protein–protein interactions, Proteins: Structure
10.1002/prot.21248 · 2007 · External reference
10.1371/journal.pone.0028766
10.1371/journal.pone.0028766 · External reference
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
10.1073/pnas.1111471108 · 2011 · External reference
Learning generative models for protein fold families, Proteins: Structure
10.1002/prot.22934 · 2011 · 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
Inference of macromolecular assemblies from crystalline state
10.1016/j.jmb.2007.05.022 · 2007 · External reference
Pisces: a protein sequence culling server
10.1093/bioinformatics/btg224 · 2003 · External reference
Noxclass: prediction of protein-protein interaction types
2006 · External reference
10.1016/s0969-2126(97)00260-8
10.1016/s0969-2126(97)00260-8 · External reference
10.1093/nar/gky1131
10.1093/nar/gky1131 · External reference
10.1016/j.ymeth.2012.07.028
10.1016/j.ymeth.2012.07.028 · External reference
Unresolved reference
External reference
10.1021/pr100618t
10.1021/pr100618t · External reference
10.1088/1361-6633/aa9965
10.1088/1361-6633/aa9965 · External reference
From dna sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase
10.1093/protein/13.1.49 · 2000 · External reference
10.1038/nature03991
10.1038/nature03991 · External reference
10.1093/protein/gzw015
10.1093/protein/gzw015 · External reference
Clustal omega for making accurate alignments of many protein sequences
10.1002/pro.3290 · 2018 · External reference
10.1038/455481a
10.1038/455481a · External reference
10.1042/bj20130545
10.1042/bj20130545 · External reference
Predicting protein–protein interactions from primary structure
10.1093/bioinformatics/17.5.455 · 2001 · External reference
Domain structural class prediction
10.1093/protein/11.7.523 · 1998 · External reference
Cdd/sparcle: the conserved domain database in 2020
10.1093/nar/gkz991 · 2020 · External reference
10.1155/2019/5238406
10.1155/2019/5238406 · External reference
Protein-protein interaction map inference using interacting domain profile pairs
10.1093/bioinformatics/17.suppl_1.s296 · 2001 · External reference
Large scale statistical prediction of protein-protein interaction by potentially interacting domain (pid) pair
2002 · External reference
Prediction of protein-protein interaction strength using domain features with supervised regression
2014 · External reference
A domain-based approach to predict protein-protein interactions
10.1186/1471-2105-8-199 · 2007 · External reference
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions
2008 · External reference
10.1146/annurev.genet.39.073003.114725
10.1146/annurev.genet.39.073003.114725 · External reference
Scoppi: a structural classification of protein–protein interfaces
10.1093/nar/gkj099 · 2006 · External reference
10.1016/j.jmb.2010.11.025
10.1016/j.jmb.2010.11.025 · External reference
10.1371/journal.pone.0065587
10.1371/journal.pone.0065587 · External reference
Detecting protein-protein interactions with a novel matrix-based protein sequence representation and support vector machines
2015 · External reference
10.1073/pnas.0607879104
10.1073/pnas.0607879104 · External reference
10.3390/ijms15023220
10.3390/ijms15023220 · External reference
10.1093/nar/gkn159
10.1093/nar/gkn159 · External reference
Act-svm: Prediction of protein-protein interactions based on support vector basis model
10.1155/2020/8866557 · 2020 · External reference
Unresolved reference
External reference
Prediction of protein-protein interaction based on deep learning feature representation and random forest
2021 · External reference
10.1021/acs.jcim.7b00028
10.1021/acs.jcim.7b00028 · External reference
Dna and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures
10.1016/0003-2670(93)80437-p · 1993 · External reference
Optimizing amino acid groupings for gpcr classification
10.1093/bioinformatics/btn382 · 2008 · External reference
Prediction of protein allergenicity using local description of amino acid sequence
10.2741/3138 · 2008 · External reference
Unresolved reference
2021 · External reference
A benchmark study of k-mer counting methods for high-throughput sequencing
2018 · External reference
10.1093/bioinformatics/bty573
10.1093/bioinformatics/bty573 · External reference
10.1093/bioinformatics/btz328
10.1093/bioinformatics/btz328 · External reference
Graph-based prediction of protein-protein interactions with attributed signed graph embedding
10.1186/s12859-020-03646-8 · 2020 · External reference
Protein–protein interaction prediction based on ordinal regression and recurrent convolutional neural networks
2021 · External reference
Deeptrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks
10.1093/bioinformatics/btab737 · 2022 · External reference
Unresolved reference
2015 · External reference
10.1039/c3mb70486f
10.1039/c3mb70486f · External reference
10.1088/1742-6596/1325/1/012089
10.1088/1742-6596/1325/1/012089 · External reference
Unresolved reference
External reference
A comprehensive survey on support vector machine classification: Applications, challenges and trends
10.1016/j.neucom.2019.10.118 · 2020 · External reference
Prediction of protein-protein interactions from protein sequence using local descriptors
10.2174/092986610791760306 · 2010 · External reference
Unresolved reference
2015 · External reference
10.1145/2939672.2939785
10.1145/2939672.2939785 · External reference
Libsvm: a library for support vector machines
10.1145/1961189.1961199 · 2011 · External reference
10.7717/peerj.7126
10.7717/peerj.7126 · External reference
Protein interactions: two methods for assessment of the reliability of high throughput observations
10.1074/mcp.m100037-mcp200 · 2002 · External reference
10.1093/bioinformatics/bth483
10.1093/bioinformatics/bth483 · External reference
10.1007/978-3-642-22456-0_37
10.1007/978-3-642-22456-0_37 · 2011 · External reference
10.1093/bioinformatics/btv077
10.1093/bioinformatics/btv077 · External reference
10.1371/journal.pone.0031826
10.1371/journal.pone.0031826 · External reference
The database of interacting proteins: 2004 update
10.1093/nar/gkh086 · 2004 · External reference
10.1093/nar/gkw937
10.1093/nar/gkw937 · External reference
10.1093/bioinformatics/bts489
10.1093/bioinformatics/bts489 · External reference
Fctp-wsrc: protein–protein interactions prediction via weighted sparse representation based classification
10.3389/fgene.2020.00018 · 2020 · External reference
10.1093/bioinformatics/btl158
10.1093/bioinformatics/btl158 · External reference
10.1093/bioinformatics/bts565
10.1093/bioinformatics/bts565 · External reference
Unresolved reference
External reference
10.1093/bioinformatics/17.3.282
10.1093/bioinformatics/17.3.282 · External reference
10.1093/nar/gky1079
10.1093/nar/gky1079 · External reference
Uniprot: a worldwide hub of protein knowledge
10.1093/nar/gky1049 · 2019 · External reference
Unresolved reference
External reference
Generating focused molecule libraries for drug discovery with recurrent neural networks
10.1021/acscentsci.7b00512 · 2018 · External reference
Generative recurrent networks for de novo drug design
10.1002/minf.201700111 · 2018 · External reference
Unresolved reference
External reference
Moleculenet: a benchmark for molecular machine learning
10.1039/c7sc02664a · 2018 · External reference
Automatic chemical design using a data-driven continuous representation of molecules
10.1021/acscentsci.7b00572 · 2018 · External reference
Grammar variational autoencoder
2017 · External reference
Unresolved reference
External reference
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence-and structure-rich era
10.1073/pnas.1314045110 · 2013 · External reference
10.7554/elife.03430
10.7554/elife.03430 · External reference
10.1038/35070613
10.1038/35070613 · External reference
10.1371/journal.pone.0015364
10.1371/journal.pone.0015364 · External reference
10.1016/j.jmb.2015.12.008
10.1016/j.jmb.2015.12.008 · External reference
Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks
10.1038/s42256-020-0222-1 · 2020 · External reference
10.1371/journal.pcbi.1008736
10.1371/journal.pcbi.1008736 · External reference
Molecular de-novo design through deep reinforcement learning
10.1186/s13321-017-0235-x · 2017 · External reference
Machine-learning-guided directed evolution for protein engineering
10.1038/s41592-019-0496-6 · 2019 · External reference
Spin2: Predicting sequence profiles from protein structures using deep neural networks, Proteins: Structure
10.1002/prot.25489 · 2018 · External reference
To improve protein sequence profile prediction through image captioning on pairwise residue distance map
10.1021/acs.jcim.9b00438 · 2019 · External reference
Unresolved reference
External reference
10.1038/s41592-018-0138-4
10.1038/s41592-018-0138-4 · External reference
Learning protein constitutive motifs from sequence data
10.7554/elife.39397 · 2019 · External reference
Accelerating protein design using autoregressive generative models
2019 · External reference
Unresolved reference
External reference
10.1038/s42256-021-00310-5
10.1038/s42256-021-00310-5 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
Design of metalloproteins and novel protein folds using variational autoencoders
10.1038/s41598-018-34533-1 · 2018 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Accurate de novo prediction of protein contact map by ultra-deep learning model
10.1371/journal.pcbi.1005324 · 2017 · External reference
A deep learning network approach to ab initio protein secondary structure prediction
10.1109/tcbb.2014.2343960 · 2014 · External reference
Protein secondary structure prediction using deep convolutional neural fields
2016 · External reference
Unresolved reference
External reference
10.1101/789719
10.1101/789719 · External reference
Unresolved reference
External reference
10.1016/j.cels.2020.08.016
10.1016/j.cels.2020.08.016 · External reference
Recurrent neural network model for constructive peptide design
10.1021/acs.jcim.7b00414 · 2018 · External reference
Unresolved reference
External reference
Sequence-based prediction of plant protein-protein interactions by combining discrete sine transformation with rotation forest
2021 · External reference
ippi-pseaac (cgr): Identify protein-protein interactions by incorporating chaos game representation into pseaac
10.1016/j.jtbi.2018.10.021 · 2019 · External reference
Targeting protein-protein interaction interfaces in covid-19 drug discovery, Computational and Structural
2021 · External reference
Unresolved reference
External reference
10.1038/nature04209
10.1038/nature04209 · External reference
10.1016/j.cell.2005.08.029
10.1016/j.cell.2005.08.029 · External reference
Unresolved reference
External reference
