Web Servers

WikiPDB

WikiPDB provides a Wikipedia-like interface (an extension of the Mediawiki software) for modification of files deposited in the PDB (Protein Data Bank), and discussion between scientists doing research on the same structures. Our system detects syntax errors, provides an API for semantic error checking plug-ins, and keeps track of different versions.

ProtDict

ProtDict is a UniProt-based Protein dictionary, capable of finding UniProt entries based on AC numbers, SwissProt IDs, EC numbers, 3 types of gene names, and 100 different types of database cross references.

Decomp

The PDB Structural Decomposition Tool repairs and decomposes files from the Protein Data Bank PDB formats. With our program, protein-ligand complexes are identified reliably, missing residues and atoms in chains are handled properly. Placeholders are inserted into chains for missing residues/atoms. Ligands are identified without using the HET-atom labels, properly handling modified residues and small artifacts, due to crystallization protocols. CONECT records of the ligand-atoms are computed automatically.

Nascent

The Nascent is a protein-protein physical interaction network construction tool based on gene names. Our program searches for proteins of source organism which are in physical interaction by the IntAct database. Then those proteins are assigned to their respective gene names. We use these gene names to make a correspondence between the source and the target organisms making a predicted protein-protein physical interaction network for the target organism.

Personalized PageRank Tool

We offer the Personalized PageRank Tool, a Perl script for computing personalized PageRank in protein-protein interaction networks, personalized to some important nodes (e.g., for nodes representing upregulated proteins in proteomics study).