A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins. It is a publicly available web-based database (via the Internet...

MOTIVATION We present a new concept that combines data storage and data analysis in genome research, based on an associative network memory. As an illustration, 115 000 conserved regions from over 73 000 published sequences (i.e. from the entire annotated part of the SWISSPROT sequence database) were identified and clustered by a self-organizing network. Similarity and kinship, as well as degre...

We propose a novel method for crowdsourcing a protein family database. We discuss how we intend to identify novel groupings of proteins from user sequence similarity search, and how text mining will be applied to assist in annotation of these novel groupings, and more broadly as an enrichment of protein sequence similarity search results. We intend to use entity linking to identify literature w...

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74,000 models for approximately 240 proteins. The system is accessible at http://www.caspur.it/...