MD-LAIs Software: Molecular Descriptors from Local Amino Acid Invariants version 1.0. MD-LAIs software is designed for the computation of sequence-based descriptors for proteins and peptides based on the application of aggregation operators over macromolecular vectors. The macromolecular vectors accounts for chemical, physical and structural properties of amino acids. The descriptors consider several extensions such as groups, a ponderation of amino acid contributions based on fuzzy membership functions, and a slide window to compute amino acid-level descriptors, which allow a high space of MDs. The software includes the following features:1) a data curation module, 2) a feature selection module, 3) XML projects with relevant and low redundant MDs, 4) low-dimensional lists of whole-sequence and amino acid-level MDs, 5) eight sample datasets, 6) three output formats (CSV,TXT, ARFF). This software was developed in Java programming language (JDK 8), and it uses the Chemical Development Kit (CDK) and the BioJava library. This software is a desktop-based application composed by a graphical user interface (GUI) and command line interface (CLI). The former was created to ease to the users the configuration of the parameters that compose the descriptors, while the CLI was designed to be used in high throughput environments.
Requirements: MD-LAIs is platform-independent software. It only requires Java(TM) 8u92 Runtime Environment (JRE) or superior on the operating system.
Running the portable application: Download the file "MD-LAIs_GUI.rar" to a local folder. Then uncompress the downloaded file, browse the folder MD-LAIs and run the file MD-LAIs_GUI.jar.
Help: The user manual is available as Manual.pdf. Further documentation can be found in the "Help" menu within the application.