Dataset Information

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

ABSTRACT: MOTIVATION:Template-based and template-free methods have both been widely used in predicting the structures of protein-protein complexes. Template-based modeling is effective when a reliable template is available, while template-free methods are required for predicting the binding modes or interfaces that have not been previously observed. Our goal is to combine the two methods to improve computational protein-protein complex structure prediction. RESULTS:Here, we present a method to identify and combine high-confidence predictions of a template-based method (SPRING) with a template-free method (ZDOCK). Cross-validated using the protein-protein docking benchmark version 5.0, our method (ZING) achieved a success rate of 68.2%, outperforming SPRING and ZDOCK, with success rates of 52.1% and 35.9% respectively, when the top 10 predictions were considered per test case. In conclusion, a statistics-based method that evaluates and integrates predictions from template-based and template-free methods is more successful than either method independently. AVAILABILITY AND IMPLEMENTATION:ZING is available for download as a Github repository (https://github.com/weng-lab/ZING.git). SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Vangaveti S

PROVIDER: S-EPMC7523679 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

Vangaveti Sweta S Vreven Thom T Zhang Yang Y Weng Zhiping Z

Bioinformatics (Oxford, England) 20200201 3

<h4>Motivation</h4>Template-based and template-free methods have both been widely used in predicting the structures of protein-protein complexes. Template-based modeling is effective when a reliable template is available, while template-free methods are required for predicting the binding modes or interfaces that have not been previously observed. Our goal is to combine the two methods to improve computational protein-protein complex structure prediction.<h4>Results</h4>Here, we present a method ...[more]

PMID: 31393558

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Project description:We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These procedures are readily automated and are being implemented on a genomic scale.

Dataset Information

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

Publications

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

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