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The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made. (bio.tools entry) [116]
Immunogenicity is a central aspect of vaccine development. [1] Unwanted immunogenicity is an immune response by an organism against a therapeutic antigen. This reaction leads to production of anti-drug-antibodies (ADAs), inactivating the therapeutic effects of the treatment and potentially inducing adverse effects. [2]
The Immune Epitope Database and Analysis Resource (IEDB) is a project hosted by scientists at the La Jolla Institute for Allergy and Immunology (LIAI), with support from the National Institute of Allergy and Infectious Diseases (NIAID), a part of the National Institutes of Health [permanent dead link ] (NIH), and Department of Health and Human Services (HHS).
I-TASSER is a template-based method for protein structure and function prediction. [1] The pipeline consists of six consecutive steps: 1, Secondary structure prediction by PSSpred; 2, Template detection by LOMETS [6] 3, Fragment structure assembly using replica-exchange Monte Carlo simulation [7]
GeneMark is a generic name for a family of ab initio gene prediction algorithms and software programs developed at the Georgia Institute of Technology in Atlanta.Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of ...
PASTA 2.0 [30] 2014 Web Server - PASTA 2.0: Secondary structure-related. Predicts the most aggregation-prone portions and the corresponding β-strand inter-molecular pairing for multiple input sequences. sequence top pairings and energies, mutations and protein-protein Amyloidogenic regions, energy, and beta-sheet orientation in aggregates
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex ...
In this mode the input is a project file that can be generated by the DeepView (Swiss Pdb Viewer) visualization and structural analysis tool, [4] to allow the user to examine and manipulate the target-template alignment in its structural context. In all three cases the output is a pdb file with atom coordinates of the model or a DeepView ...