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Chin. Phys. B, 2020, Vol. 29(10): 108707    DOI: 10.1088/1674-1056/abb659
Special Issue: SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids
Topical Review—Modeling and simulations for the structures and functions of proteins and nucleic acids Prev   Next  

Review of multimer protein–protein interaction complex topology and structure prediction

Daiwen Sun(孙黛雯)1, Shijie Liu(刘世婕)1, and Xinqi Gong(龚新奇)1,2,
1 Mathematics Intelligence Application Laboratory, Institute for Mathematical Sciences, Renmin University of China, Beijing 100872, China
2 Beijing Advanced Innovation Center for Structural Biology, Tshinghua University, Beijing 100094, China

Protein–protein interactions (PPI) are important for many biological processes. Theoretical understanding of the structurally determining factors of interaction sites will help to understand the underlying mechanism of protein–protein interactions. At the same time, understanding the complex structure of proteins helps to explore their function. And accurately predicting protein complexes from PPI networks helps us understand the relationship between proteins. In the past few decades, scholars have proposed many methods for predicting protein interactions and protein complex structures. In this review, we first briefly introduce the methods and servers for predicting protein interaction sites and interface residue pairs, and then introduce the protein complex structure prediction methods including template-based prediction and template-free prediction. Subsequently, this paper introduces the methods of predicting protein complexes from the PPI network and the method of predicting missing links in the PPI network. Finally, it briefly summarizes the application of machine/deep learning models in protein structure prediction and action site prediction.

Keywords:  protein complex prediction      protein-protein interaction  
Received:  29 June 2020      Revised:  31 August 2020      Published:  05 October 2020
PACS: (Protein-protein interactions)  
  01.50.hv (Computer software and software reviews)  
Corresponding Authors:  Corresponding author. E-mail:   
About author: 
†Corresponding author. E-mail:
* Project supported by the National Natural Science Foundation of China (Grant No. 31670725).

Cite this article: 

Daiwen Sun(孙黛雯), Shijie Liu(刘世婕), and Xinqi Gong(龚新奇)† Review of multimer protein–protein interaction complex topology and structure prediction 2020 Chin. Phys. B 29 108707

Fig. 1.  

The main content of protein interaction calculation.

Fig. 2.  

Statistics of protein multimers in PDB database.

Optimization algorithms Programs
Fast Fourier transformation ZDOCK; GRAMM; DOT; SmoothDock; ClusPro; MolFit; FTDock; 3D-Dock; PIPER; pyDock; HDOCK; SDOCK; HEX; FRODOCK; InterEvDock; MDockPP; CoDockPP; HSYMDOCK; SAM
Monte Carlo RosettaDock; ICM-DOCK; HADDOCK; ATTRACT
Genetic algorithm DARWIN; Multi-LZerD; AutoDock
Table 1.  

Classification of optimization algorithms applied by protein protein docking approached.

Fig. 3.  

The system of protein complex prediction.

Methods Description Advantages Limits
Interface residue pair prediction ComplexContact; RaptorX-Contact; RaptorX-Property; Gremlin; DNCON2; PSICOV; FreeContact; LSTM; LSTM with Graph Representation Direct evolutionary coupling analysis (DCA), machine learning and deep learning methods Interfacial residue pair prediction can help subsequent protein complex structure predictions, such as docking.Protein contact map prediction can help reconstruct the three-dimensional structure of protein complexes. The accuracy of interface residues for prediction needs to be improved.
Protein structure prediction Template-free ZDOCK; GRAMM; DOT; SmoothDock; ClusPro; MolFit; FTDock; 3D-Dock; PIPER; pyDock; HDOCK; SDOCK; HEX; FRODOCK; InterEvDock; MDockPP; CoDockPP; HSYMDOCK; SAM; RosettaDock; ICM-DOCK; HADDOCK; ATTRACT; DARWIN; Multi-LZerD; AutoDock The search strategies of these methods are mainly FFT, GA and MC. Protein docking can give all possible complex structures, some of which can also dock Cn and Dn complexes. Designing an effective scoring function to sort the docking structure remains to be further explored.
Template-based InterPreTS; Multimeric threading approach; M-Tasser; PISA; ProtCID Using sequence or structure similarity to model protein complexes with known structures. Template-based methods mainly reduce the possible structure by restricting the direction of protein binding. This method is more efficient than docking and can be applied to larger-scale protein complex prediction. For proteins without a template, the structure of the complex cannot be predicted.
Protein complex prediction from PPI networks Complex prediction based on PPI network clustering MCODE; MCL; SPC; LCMA; SuperComplex; BN; CFinder; DPClus; IPCA; CMC; ClusterONE; HACO The protein complex is part of a known PPI network, that is, the graph composed of protein complexes and their interactions is a subgraph of the PPI network. Some of these methods only use the PPI network for clustering, and some use additional biological information, including structure, function, organization and co-evolution infornation, etc. The proteins that may form complexes can only be picked out from the existing PPI network.
Complex interaction link prediction from PPI network GGA; HAC; ECT; RWR; MDS; Link-weighted PPI Methods to predict actual links in the network include public neighbors-based methods and distance-based methods. This type of method predicts possible protein--protein interactions based on existing network information. Public neighbors-based methods have limited effect on sparse networks.
Table 2.  

The summary of protein complex calculations.

Janin J 2010 Molecular bioSystems 6 2351 DOI: 10.1039/c005060c
Sudha G, Nussinov R, Srinivasan N 2014 Prog. Biophys. Mol. Biol. 116 141 DOI: 10.1016/j.pbiomolbio.2014.07.004
Zhou T M, Wang S, Xu J 2018 bioRxiv DOI: 10.1101/240754v3
Zeng H, Wang S, Zhou T, Zhao F, Li X, Wu Q, Xu J 2018 Nucleic Acids Research 46 W432 DOI: 10.1093/nar/gky420
Ching T, Himmelstein D S, Beaulieu-Jones B K et al. 2018 J. R. Soc. Interface 15 20170387 DOI: 10.1098/rsif.2017.0387
Wang S, Sun S, Li Z, Zhang R, Xu J 2017 PLoS Comput. Biol. 13 e1005324 DOI: 10.1371/journal.pcbi.1005324
Wang S, Li W, Liu S, Xu J 2016 Nucleic Acids Research 44 W430 DOI: 10.1093/nar/gkw306
Kamisetty H, Ovchinnikov S, Baker D 2013 Proc. Natl. Acad. Sci. USA 110 15674 DOI: 10.1073/pnas.1314045110
Balakrishnan S, Kamisetty H, Carbonell J G, Lee S I, Langmead C J 2011 Proteins 79 1061 DOI: 10.1002/prot.22934
Ovchinnikov S, Kamisetty H, Baker D 2014 Elife 3 e02030 DOI: 10.7554/eLife.02030.002
Adhikari B, Hou J, Cheng J 2018 Bioinformatics 34 1466 DOI: 10.1093/bioinformatics/btx781
Jones D T, Buchan D W, Cozzetto D, Pontil M 2012 Bioinformatics 28 184 DOI: 10.1093/bioinformatics/btr638
Kaján L, Hopf T A, Kalaš M, Marks D S, Rost B 2014 BMC Bioinformatics 15 85 DOI: 10.1186/1471-2105-15-85
Wang S, Li W, Zhang R, Liu S, Xu J 2016 Nucleic Acids Res. 44 W361 DOI: 10.1093/nar/gkw307
Xu G, Wang Q, Ma J 2020 Journal of Chemical Theory and Computation 16 3970 DOI: 10.1021/acs.jctc.0c00186
Zhao Z, Gong X 2019 IEEEACM Transactions on Computational Biology and Bioinformatics 16 1753 DOI: 10.1109/TCBB.2017.2706682
Sun D, Gong X 2020 Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 140504 DOI: 10.1016/j.bbapap.2020.140504
Liu J, Gong X 2019 BMC Bioinformatics 20 609 DOI: 10.1186/s12859-019-3199-1
Vreven T, Hwang H, Pierce B G, Weng Z 2014 Brief Bioinform 15 169 DOI: 10.1093/bib/bbt047
Zhang Q, Feng T, Xu L, Sun H, Pan P, Li Y, Li D, Hou T 2016 Curr. Drug Targets 17 1586 DOI: 10.2174/1389450117666160112112640
Ritchie D W, Kemp G J 2000 Proteins: Structure, Function, and Bioinformatics 39 178 DOI: 10.1002/(ISSN)1097-0134
Lee K, Czaplewski C, Kim S Y, Lee J 2005 Journal of Computational Chemistry 26 78 DOI: 10.1002/(ISSN)1096-987X
Ritchie D W 2003 Proteins: Structure, Function, and Bioinformatics 52 98 DOI: 10.1002/(ISSN)1097-0134
Pierce B, Tong W, Weng Z 2005 Bioinformatics 21 1472 DOI: 10.1093/bioinformatics/bti229
Chen R, Li L, Weng Z 2003 Proteins 52 80 DOI: 10.1002/(ISSN)1097-0134
André I, Bradley P, Wang C, Baker D 2007 Proc. Natl. Acad. Sci. USA 104 17656 DOI: 10.1073/pnas.0702626104
Comeau S R, Gatchell D W, Vajda S, Camacho C J 2004 Bioinformatics 20 45 DOI: 10.1093/bioinformatics/btg371
Yan Y, Tao H, He J, Huang S Y 2020 Nature Protocols 15 1829 DOI: 10.1038/s41596-020-0312-x
Yan Y, Zhang D, Zhou P, Li B, Huang S Y 2017 Nucleic Acids Res. 45 W365 DOI: 10.1093/nar/gkx407
Yan Y, Tao H, Huang S Y 2018 Nucleic Acids Res. 46 W423 DOI: 10.1093/nar/gky398
Ritchie D W, Grudinin S 2016 Journal of Applied Crystallography 49 158 DOI: 10.1107/S1600576715022931
Yu H, Luscombe N M, Lu H X, Zhu X, Xia Y, Han J D J, Bertin N, Chung S, Vidal M, Gerstein M 2004 Genome Research 14 1107 DOI: 10.1101/gr.1774904
Aloy P, Russell R B 2002 Proc. Natl. Acad. Sci. USA 99 5896 DOI: 10.1073/pnas.092147999
Aloy P, Russell R B 2003 Bioinformatics 19 161 DOI: 10.1093/bioinformatics/19.1.161
Lu L, Lu H, Skolnick J 2002 Proteins 49 350 DOI: 10.1002/(ISSN)1097-0134
Chen H, Skolnick J 2008 Biophys J. 94 918 DOI: 10.1529/biophysj.107.114280
Launay G, Simonson T 2008 BMC Bioinformatics 9 427 DOI: 10.1186/1471-2105-9-427
Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin A C, Bork P, Superti-Furga G, Serrano L 2004 Science 303 2026 DOI: 10.1126/science.1092645
Nye T M W, Berzuini C, Gilks W R, Babu M M, Teichmann S A 2004 Bioinformatics 21 993 DOI: 10.1093/bioinformatics/bti086
Krissinel E, Henrick K 2007 Journal of Molecular Biology 372 774 DOI: 10.1016/j.jmb.2007.05.022
Xu Q, Dunbrack R L 2010 Nucleic Acids Res. 39 D761 DOI: 10.1093/nar/gkq1059
Yu H, Braun P, Yildirim M A, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual J F, Dricot A, Vazquez A, Murray R R, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet A S, Motyl A, Hudson M E, Park J, Xin X, Cusick M E, Moore T, Boone C, Snyder M, Roth F P, Barabási A L, Tavernier J, Hill D E, Vidal M 2008 Science 322 104 DOI: 10.1126/science.1158684
Tarassov K, Messier V, Landry C R, Radinovic S, Serna Molina M M, Shames I, Malitskaya Y, Vogel J, Bussey H, Michnick S W 2008 Science 320 1465 DOI: 10.1126/science.1153878
Krogan N J, Cagney G, Yu H et al. 2006 Nature 440 637 DOI: 10.1038/nature04670
Gavin A C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen L J, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier M A, Hoffman V, Hoefert C, Klein K, Hudak M, Michon A M, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick J M, Kuster B, Bork P, Russell R B, Superti-Furga G 2006 Nature 440 631 DOI: 10.1038/nature04532
Pržulj N 2011 Bioessays 33 115 DOI: 10.1002/bies.v33.2
Yu H, Kim P M, Sprecher E, Trifonov V, Gerstein M 2007 PLoS Comput. Biol. 3 e59 DOI: 10.1371/journal.pcbi.0030059
Jeong H, Mason S P, Barabási A L, Oltvai Z N 2001 Nature 411 41 DOI: 10.1038/35075138
Han J D J, Bertin N, Hao T, Goldberg D S, Berriz G F, Zhang L V, Dupuy D, Walhout A J M, Cusick M E, Roth F P, Vidal M 2004 Nature 430 88 DOI: 10.1038/nature02555
Wang J, Li M, Deng Y, Pan Y 2010 BMC Genomics 11 3 S10 DOI: 10.1186/1471-2164-11-s3-s10
Ulitsky I, Shamir R 2009 Bioinformatics 25 1158 DOI: 10.1093/bioinformatics/btp118
Sharan R, Ulitsky I, Shamir R 2007 Mol. Syst. Biol. 3 88 DOI: 10.1038/msb4100129
Lee K, Chuang H Y, Beyer A, Sung M K, Huh W K, Lee B, Ideker T 2008 Nucleic Acids Res. 36 e136 DOI: 10.1186/1471-2164-11-s3-s10
King A D, Przulj N, Jurisica I 2004 Bioinformatics 20 3013 DOI: 10.1093/bioinformatics/bth351
Friedel C C, Krumsiek J, Zimmer R 2009 J. Comput. Biol. 16 971 DOI: 10.1089/cmb.2009.0023
Chua H N, Sung W K, Wong L 2006 Bioinformatics 22 1623 DOI: 10.1093/bioinformatics/btl145
Bader G D, Hogue C W V 2002 Nature Biotechnology 20 991 DOI: 10.1038/nbt1002-991
Asthana S, King O D, Gibbons F D, Roth F P 2004 Genome Research 14 1170 DOI: 10.1101/gr.2203804
Kim Y A, Wuchty S, Przytycka T M 2011 PLoS Comput. Biol. 7 e1001095 DOI: 10.1371/journal.pcbi.1001095
Ideker T, Sharan R 2008 Genome Research 18 644 DOI: 10.1101/gr.071852.107
Hidalgo C A, Blumm N, Barabási A L, Christakis N A 2009 PLoS Comput. Biol. 5 e1000353
Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan N J, Karp R M, Ideker T 2009 PLoS Genet. 5 e1000782
Chuang H Y, Lee E, Liu Y T, Lee D, Ideker T 2007 Molecular Systems Biology 3 140 DOI: 10.1038/msb4100180
Huang H, Jedynak B M, Bader J S 2007 PLoS Comput. Biol. 3 e214 DOI: 10.1371/journal.pcbi.0030214
Lei C, Ruan J 2012 IEEE International Conference on Bioinformatics and Biomedicine 4–7 October, 2012 1 6
Srihari S, Yong C H, Wong L 2017 Computational prediction of protein complexes from protein interaction networks Association for Computing Machinery DOI: 10.1145/3064650
Bader G D, Hogue C W 2003 BMC bioinformatics 4 2 DOI: 10.1186/1471-2105-4-2
Pereira Leal J B, Enright A J, Ouzounis C A 2004 PROTEINS: Structure, Function, and Bioinformatics 54 49 DOI: 10.1002/prot.10505
Brohee S, Van Helden J 2006 BMC Bioinformatics 7 488 DOI: 10.1186/1471-2105-7-488
Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak S J 2007 Proteomics 7 944 DOI: 10.1002/(ISSN)1615-9861
Blatt M, Wiseman S, Domany E 1996 Phys. Rev. Lett. 76 3251 DOI: 10.1103/PhysRevLett.76.3251
Getz G, Vendruscolo M, Sachs D, Domany E 2002 Proteins: Structure, Function, and Bioinformatics 46 405 DOI: 10.1002/(ISSN)1097-0134
Getz G, Levine E, Domany E 2000 Proc. Natl. Acad. Sci. USA 97 12079 DOI: 10.1073/pnas.210134797
Spirin V, Mirny L A 2003 Proc. Natl. Acad. Sci. USA 100 12123 DOI: 10.1073/pnas.2032324100
Li X L, Foo C S, Tan S H, Ng S K 2005 Genome Informatics 16 260 DOI: 10.11234/gi1990.16.2_260
Qi Y, Balem F, Faloutsos C, Klein-Seetharaman J, Bar-Joseph Z 2008 Bioinformatics 24 i250 DOI: 10.1093/bioinformatics/btn164
Yong C H, Liu G, Chua H N, Wong L BMC Systems Biology S13 DOI: 10.1186/1752-0509-6-S2-S13
Srihari S, Leong H W 2012 International Journal of Bioinformatics Research and Applications 8 286 DOI: 10.1504/IJBRA.2012.048962
Adamcsek B, Palla G, Farkas I J, Derenyi I, Vicsek T 2006 Bioinformatics 22 1021 DOI: 10.1093/bioinformatics/btl039
Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S 2006 BMC Bioinformatics 7 207 DOI: 10.1186/1471-2105-7-207
Li M, Chen J E, Wang J X, Hu B, Chen G 2008 BMC Bioinformatics 9 398 DOI: 10.1186/1471-2105-9-398
Liu G, Wong L, Chua H N 2009 Bioinformatics 25 1891 DOI: 10.1093/bioinformatics/btp311
Nepusz T, Yu H, Paccanaro A 2012 Nat. Methods 9 471 DOI: 10.1038/NMETH.1938
Wang H, Kakaradov B, Collins S R, Karotki L, Fiedler D, Shales M, Shokat K M, Walther T C, Krogan N J, Koller D 2009 Mol. Cell Proteomics 8 1361 DOI: 10.1074/mcp.M800490-MCP200
Tong H, Faloutsos C, Pan J Y Sixth international conference on data mining (ICDM’06) 613 622
Radicchi F, Castellano C, Cecconi F, Loreto V, Parisi D 2004 Proc. Natl. Acad. Sci. USA 101 2658 DOI: 10.1073/pnas.0400054101
Li A, Horvath S 2007 Bioinformatics 23 222 DOI: 10.1093/bioinformatics/btl581
Fouss F, Pirotte A, Renders J, Saerens M 2007 IEEE Transactions on Knowledge and Data Engineering 19 355 DOI: 10.1109/TKDE.2007.46
Lü L, Zhou T 2011 Physica A 390 1150 DOI: 10.1016/j.physa.2010.11.027
Wang C, Ding C, Yang Q, Holbrook S R 2007 Genome Biol. 8 R271 DOI: 10.1186/gb-2007-8-12-r271
Fang Y, Benjamin W, Sun M, Ramani K 2011 PLoS One 6 e19349 DOI: 10.1371/journal.pone.0019349
Xu Q, Xiang E W, Yang Q 2011 Proteomics 11 3818 DOI: 10.1002/pmic.201100146
Park Y, Bader J S 2011 BMC Bioinformatics 12 S44 DOI: 10.1186/1471-2105-12-S1-S44
Kuchaiev O, Rasajski M, Higham D J, Przulj N 2009 PLoS Comput. Biol. 5 e1000454 DOI: 10.1371/journal.pcbi.1000454
Lei C, Ruan J 2012 Bioinformatics 29 355 DOI: 10.1093/bioinformatics/bts688
Wang L, Hu K, Tang Y 2014 Current Bioinformatics 9 246 DOI: 10.2174/1574893609666140516005740
Bartoli L, Capriotti E, Fariselli P, Martelli P L, Casadio R 2008 Methods Mol. Biol. 413 199 DOI: 10.1371/journal.pcbi.1000454
Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R 2008 IEEEACM Trans. Comput. Biol. Bioinform. 5 357 DOI: 10.1109/tcbb.2008.27
Vendruscolo M, Kussell E, Domany E 1997 Fold Des. 2 295 DOI: 10.1016/S1359-0278(97)00041-2
Breu H, Kirkpatrick D G 1998 Computational Geometry 9 3 DOI: 10.1016/S0925-7721(97)00014-X
Zhang C, Mortuza S M, He B, Wang Y, Zhang Y 2018 Proteins 86 1 136 DOI: 10.1002/prot.25414
Baú D, Martin A J M, Mooney C, Vullo A, Walsh I, Pollastri G 2006 BMC Bioinformatics 7 402 DOI: 10.1186/1471-2105-7-402
Kukic P, Mirabello C, Tradigo G, Walsh I, Veltri P, Pollastri G 2014 BMC Bioinformatics 15 6 DOI: 10.1186/1471-2105-15-6
Walsh I, Baù D, Martin A J M, Mooney C, Vullo A, Pollastri G 2009 BMC Structural Biology 9 5 DOI: 10.1186/1472-6807-9-5
Fariselli P, Casadio R 2001 Bioinformatics 17 957 DOI: 10.1093/bioinformatics/17.10.957
Martelli P L, Fariselli P, Malaguti L, Casadio R 2002 Protein Engineering, Design and Selection 15 951 DOI: 10.1093/protein/15.12.951
Ceroni A, Passerini A, Vullo A, Frasconi P 2006 Nucleic Acids Res. 34 W177 DOI: 10.1093/nar/gkl266
Tsai C H, Chen B J, Chan C H, Liu H L, Kao C Y 2005 Bioinformatics 21 4416 DOI: 10.1093/bioinformatics/bti715
Vullo A, Frasconi P 2004 Bioinformatics 20 653 DOI: 10.1093/bioinformatics/btg463
Ferrè F, Clote P 2005 Nucleic Acids Res 33 W230 DOI: 10.1093/nar/gki412
Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin A 2018 Proteins 86 1 51 DOI: 10.1002/prot.25407
Seemayer S, Gruber M, Söding J 2014 Bioinformatics 30 3128 DOI: 10.1093/bioinformatics/btu500
Jones D T, Kandathil S M 2018 Bioinformatics 34 3308 DOI: 10.1093/bioinformatics/bty341
Hanson J, Paliwal K, Litfin T, Yang Y, Zhou Y 2018 Bioinformatics 34 4039 DOI: 10.1093/bioinformatics/bty481
Senior A W, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C, Žídek A, Nelson A W, Bridgland A 2019 Proteins: Structure, Function, and Bioinformatics 87 1141 DOI: 10.1002/prot.v87.12
Dong Q, Wang X, Lin L, Guan Y 2007 BMC Bioinformatics 8 147 DOI: 10.1186/1471-2105-8-147
Minhas F u A A, Geiss B J, Ben-Hur A 2014 Proteins 82 1142 DOI: 10.1002/prot.v82.7
Zellner H, Staudigel M, Trenner T, Bittkowski M, Wolowski V, Icking C, Merkl R 2012 Proteins 80 154 DOI: 10.1002/prot.23172
Wang B, Chen P, Huang D S, Li J J, Lok T M, Lyu M R 2006 FEBS Lett. 580 380 DOI: 10.1016/j.febslet.2005.11.081
Bradford J R, Westhead D R 2005 Bioinformatics 21 1487 DOI: 10.1093/bioinformatics/bti242
Koike A, Takagi T 2004 Protein Eng. Des. Sel. 17 165 DOI: 10.1093/protein/gzh020
Sriwastava B K, Basu S, Maulik U 2015 J. Biosci. 40 809 DOI: 10.1007/s12038-015-9564-y
Singh G, Dhole K, Pai P P, Mondal S 2014 SPRINGS: prediction of protein–protein interaction sites using artificial neural networks Report No. 2167–9843 DOI: 10.7287/peerj.preprints.266v2
Ofran Y, Rost B 2007 Bioinformatics 23 e13 DOI: 10.1093/bioinformatics/btl303
Chen H, Zhou H X 2005 Proteins 61 21 DOI: 10.1002/prot.20514
Ofran Y, Rost B 2003 FEBS Lett. 544 236 DOI: 10.1016/S0014-5793(03)00456-3
Fariselli P, Pazos F, Valencia A, Casadio R 2002 Eur. J. Biochem. 269 1356 DOI: 10.1046/j.1432-1033.2002.02767.x
Zhou H X, Shan Y 2001 Proteins: Structure, Function, and Bioinformatics 44 336 DOI: 10.1002/(ISSN)1097-0134
Bradford J R, Needham C J, Bulpitt A J, Westhead D R 2006 J. Mol. Biol. 362 365 DOI: 10.1016/j.jmb.2006.07.028
Neuvirth H, Raz R, Schreiber G 2004 J. Mol. Biol. 338 181 DOI: 10.1016/j.jmb.2004.02.040
Geng H, Lu T, Lin X, Liu Y, Yan F 2015 Biochemistry Research International 2015 978193 DOI: 10.1155/2015/978193
Murakami Y, Mizuguchi K 2010 Bioinformatics 26 1841 DOI: 10.1093/bioinformatics/btq302
Chen X W, Jeong J C 2009 Bioinformatics 25 585 DOI: 10.1093/bioinformatics/btp039
Northey T C, Barešić A, Martin A C R 2018 Bioinformatics 34 223 DOI: 10.1093/bioinformatics/btx585
Li B Q, Feng K Y, Chen L, Huang T, Cai Y D 2012 PLoS One 7 e43927 DOI: 10.1371/journal.pone.0043927
Sikić M, Tomić S, Vlahovicek K 2009 PLoS Comput. Biol. 5 e1000278 DOI: 10.1371/journal.pcbi.1000278
Wei Z S, Yang J Y, Shen H B, Yu D J 2015 IEEE Trans. Nanobioscience 14 746 DOI: 10.1109/TNB.2015.2475359
Li M H, Lin L, Wang X L, Liu T 2007 Bioinformatics 23 597 DOI: 10.1093/bioinformatics/btl660
Wang D D, Wang R, Yan H 2014 Neurocomputing 128 258 DOI: 10.1016/j.neucom.2012.12.062
Dhole K, Singh G, Pai P P, Mondal S 2014 J. Theor. Biol. 348 47 DOI: 10.1016/j.jtbi.2014.01.028
Jia J, Liu Z, Xiao X, Liu B, Chou K C 2016 J. Biomol. Struct. Dyn. 34 1946 DOI: 10.1080/07391102.2015.1095116
Deng L, Guan J, Dong Q, Zhou S 2009 BMC Bioinformatics 10 426 DOI: 10.1186/1471-2105-10-426
Chen P, Li J 2010 BMC Bioinformatics 11 402 DOI: 10.1186/1471-2105-11-402
Du X, Sun S, Hu C, Li X, Xia J 2016 J. Biol. Res. (Thessalon) 23 10 DOI: 10.1186/s40709-016-0046-7
Krizhevsky A, Sutskever I, Hinton G E Advances in Neural Information Processing Systems 1097 1105 DOI: 10.1186/s40709-016-0046-7
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