Offers a framework for processing commonly used biological data. BioJava consists of several independent modules built using Maven. The software contains state-of-the-art algorithms, several file parsers, and data models to perform various calculations and to facilitate working with the standard data formats. It enables application development and analysis.
Allows users to extract significant motifs from large data sets, like groups of proteins that share a common biological function and tandem mass spectrometry (MS/MS) post-translational modification data. Motif-x can extract over-represented patterns from any sequence data set. It permits users to import their data and also to download results that use Web browsers on essentially any Web-compatible computer.
Allows prediction of potential protein post-translational modifications (PTMs). FindMod is able to retrieve potential single amino acid substitutions in peptides. It can analyze peptide mass fingerprinting results of known proteins for the presence of 22 types of PTMs of discrete mass.
Aims to optimize drug discovery process. BIOVIA Discovery Studio is a comprehensive suite of science applications. It offers a visualization and collaboration framework that includes a comprehensive science portfolio. It provides several tools for simulations, for macromolecule design and analysis, for antibody development, for structure-based design (SBD), for fragment-based design (FBD) or for pharmacophore and ligand-based design.
Predicts phosphorylation sites in an organism of interest. DAPPLE represents an alternative method to machine-learning approaches and is based on a direct homology-based approach. It employs experimentally-determined phosphorylation sites in organisms to predict phosphorylation. This tool uses BLAST to search for similar 15-mer peptides in the proteome of the target organism. It can report descriptions of the query and matching proteins or the locations of the putative phosphorylation sites in the protein sequences.
Provides a systematic and sophisticated platform for proteomic post-translational modifications (PTMs) research. SysPTM is a systematic resource for PTM research consisting of a PTM database and four analysis tools (PTMBlast, PTMPathway, PTMPhylog, PTMCluster). The multi-organism feature of this application makes it extremely useful for comparative modificomics. Additionally, multi-site and multi-type modification can be investigated.