GPSRdocker: Integration of all software from Raghava group in docker

Welcome to the official documentation for GPSRdocker, a comprehensive, lightweight, and isolated platform designed to provide a wide range of computational tools for bioinformatics researchers. This resource integrates over 65 standalone software packages predominantly developed by Dr. Gajendra P.S.Raghava's group over the last two decades. Official Website: https://webs.iiitd.edu.in/gpsrdocker/Docker Hub: raghavagps/gpsrdocker Citation Agrawal P, Kumar R, Usmani SS, Dhall A, Patiyal S, Sharma N, et al. (2019).GPSRdocker: A Docker-based Resource for Genomics, Proteomics and Systems biology. bioRxiv 827766.https://doi.org/10.1101/827766 Zenodo:-https://github.com/Manish-IIITD-repository/GPSRdocker About the Platform GPSRdocker addresses the challenges of traditional web-based services, such as internet speed limitations, computing power restrictions, and data security concerns.By utilizing Docker containerization, it provides a portable environment that ensures hardware/software compatibility and eliminates complex installation dependencies. The container is categorized into three main components: General Scripts: Small Perl and Python programs for generating features like protein composition. Supporting Software: Integrated packages for data processing and model development, including PSI-BLAST, CD-HIT, WEKA, and SVMlight. Standalone Prediction Packages: Core software for predicting functions or classes of biomolecules across six major categories. Key Categories and Standalone Tools [Image of protein structure prediction types] 1. Protein Structure Prediction Tools to predict alpha/beta/gamma turns, transmembrane regions, and surface accessibility. ALPHApred: Predicts alpha-turns using neural networks. SARpred: Predicts real-value solvent accessibility. TBBpred: Predicts transmembrane beta-barrel regions. 2. Functional Annotation of Proteins Methods for predicting subcellular localization and protein binding properties. ALGpred: Predicts allergenic proteins and maps IgE epitopes. ESLpred2: Advanced subcellular localization for eukaryotic proteins. RNApred: Predicts RNA-binding proteins. 3. Vaccinomics Tools for immunogenomics and epitope-based vaccine design. abcpred: Mapping B-cell epitopes using neural networks. ProPred / ProPred1: Predicts MHC Class-II and Class-I binding sites. vaxinpad: Designing peptide-based vaccine adjuvants. 4. Genomics Biomarker identification and genome annotation. cancercsp: Gene expression-based biomarkers for renal cancer. desirm: Designing highly efficient siRNAs. 5. BioDrugs In silico screening for bioactive drugs and therapeutic peptides. AntiCP: Prediction and design of anticancer peptides. ToxinPred: Predicting and designing toxic/non-toxic peptides. AntiTbPred: Predicting peptides with bactericidal activity against Mycobacterium. 6. Interactome Study of molecular interactions among proteins and small molecules. ATPint / GTPbinder: Identification of ATP and GTP binding sites. GlycoEP / GlycoPP: Prediction of glycosylation sites in eukaryotes and prokaryotes. Implementation & Usage GPSRdocker provides a flexible platform that can run on any operating system or be ported to the cloud. Basic Commands: Pull the Image:docker pull raghavagps/gpsrdocker Run the Container:docker run -i -t raghavagps/gpsrdocker Install Software Packages:Inside the image, run: /gpsr/gpsr_install.pl Key Advantages Data Security: Standalone operation allows researchers to keep confidential data local. High Throughput: Capable of processing large datasets that typically exceed webserver limits. No Internet Required: Once the image is pulled, all tools function offline. Contact & Support Prof. Gajendra P.S. [cite_start]Raghava Head, Department of Computational BiologyIndraprastha Institute of Information Technology (IIIT-Delhi), India.Email: [e-mail] License This resource is available free for academic use under the aCC-BY 4.0 International license.