Dataset Information

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

ABSTRACT:

Motivation

MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency.

Availability and implementation

The program is available at http://wanglab.ucsd.edu/MIEC-SVM CONTACT: : wei-wang@ucsd.edu

Supplementary information

Supplementary data available at Bioinformatics online.

SUBMITTER: Li N

PROVIDER: S-EPMC4907390 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Publications

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

Li Nan N Ainsworth Richard I RI Wu Meixin M Ding Bo B Wang Wei W

Bioinformatics (Oxford, England) 20151114 6

<h4>Motivation</h4>MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational ...[more]

PMID: 26568623

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Project description:The ability to predict a protein's three-dimensional conformation represents a crucial starting point for investigating evolutionary connections with other members of the corresponding protein family, examining interactions with other proteins, and potentially utilizing this knowledge for the purpose of rational drug design. In this work, we evaluated the feasibility of improving AlphaFold2's three-dimensional protein predictions by developing a novel pipeline (AlphaMod) that incorporates AlphaFold2 with MODELLER, a template-based modeling program. Additionally, our tool can drive a comprehensive quality assessment of the tertiary protein structure by incorporating and comparing a set of different quality assessment tools. The outcomes of selected tools are combined into a composite score (BORDASCORE) that exhibits a meaningful correlation with GDT_TS and facilitates the selection of optimal models in the absence of a reference structure. To validate AlphaMod's results, we conducted evaluations using two distinct datasets summing up to 72 targets, previously used to independently assess AlphaFold2's performance. The generated models underwent evaluation through two methods: i) averaging the GDT_TS scores across all produced structures for a single target sequence, and ii) a pairwise comparison of the best structures generated by AlphaFold2 and AlphaMod. The latter, within the unsupervised setups, shows a rising accuracy of approximately 34% over AlphaFold2. While, when considering the supervised setup, AlphaMod surpasses AlphaFold2 in 18% of the instances. Finally, there is an 11% correspondence in outcomes between the diverse methodologies. Consequently, AlphaMod's best-predicted tertiary structures in several cases exhibited a significant improvement in the accuracy of the predictions with respect to the best models obtained by AlphaFold2. This pipeline paves the way for the integration of additional data and AI-based algorithms to further improve the reliability of the predictions.

Dataset Information

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

Motivation

Availability and implementation

Supplementary information

Publications

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

Similar Datasets

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