Chinese Physics B, Volume. 29, Issue 10, (2020)
Review of multimer protein–protein interaction complex topology and structure prediction
Figures & Tables(5)
Table 1. Classification of optimization algorithms applied by protein protein docking approached.
View tableView in ArticleTable 1. Classification of optimization algorithms applied by protein protein docking approached.
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 2. The summary of protein complex calculations.
View tableView in ArticleTable 2. The summary of protein complex calculations.
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.
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Daiwen Sun, Shijie Liu, Xinqi Gong. Review of multimer protein–protein interaction complex topology and structure prediction[J]. Chinese Physics B, 2020, 29(10):
Paper Information
Received: Jun. 29, 2020
Accepted: --
Published Online: Apr. 21, 2021
The Author Email: Gong Xinqi (xinqigong@ruc.edu.cn)
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