Dataset Information

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

ABSTRACT: The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run "big data" batch jobs; to generate predictions using modified protein data bank (PDB) structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models.

SUBMITTER: Masso M

PROVIDER: S-EPMC4150472 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

Masso Majid M Vaisman Iosif I II

Advances in bioinformatics 20140817

The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the othe ...[more]

PMID: 25197272

Similar Datasets

Project description:This work aims to provide a reliable and intelligent prediction model for future trends in sharing economy. Moreover, it presents valuable insights for decision-making and policy development by relevant governmental bodies. Furthermore, the study introduces a predictive system that incorporates an enhanced Harris Hawk Optimization (HHO) algorithm and a K-Nearest Neighbor (KNN) forecasting framework. The method utilizes an improved simulated annealing mechanism and a Gaussian bare bone structure to improve the original HHO, termed SGHHO. To achieve optimal prediction performance and identify essential features, a refined simulated annealing mechanism is employed to mitigate the susceptibility of the original HHO algorithm to local optima. The algorithm employs a mechanism that boosts its global search ability by generating fresh solution sets at a specific likelihood. This mechanism dynamically adjusts the equilibrium between the exploration and exploitation phases, incorporating the Gaussian bare bone strategy. The best classification model (SGHHO-KNN) is developed to mine the key features with the improvement of both strategies. To assess the exceptional efficacy of the SGHHO algorithm, this investigation conducted a series of comparative trials employing the function set of IEEE CEC 2014. The outcomes of these experiments unequivocally demonstrate that the SGHHO algorithm outperforms the original HHO algorithm on 96.7% of the functions, substantiating its remarkable superiority. The algorithm can achieve the optimal value of the function on 67% of the tested functions and significantly outperforms other competing algorithms. In addition, the key features selected by the SGHHO-KNN model in the prediction experiment, including " Form of sharing economy in your region " and " Attitudes to the sharing economy ", are important for predicting the future trends of the sharing economy in this study. The results of the prediction demonstrate that the proposed model achieves an accuracy rate of 99.70% and a specificity rate of 99.38%. Consequently, the SGHHO-KNN model holds great potential as a reliable tool for forecasting the forthcoming trajectory of the sharing economy.

Project description:The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

Dataset Information

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

Publications

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets