Software

This page introduces the software and the Web services developed by the Computational Biology Laboratory.

FUJISAN

This program predicts whether a pair of enzymes catalyze the same reaction on the same substrate based on the sequence and the structure similarities.

Available at: https://github.com/sfujita0601/FUJISAN

pdb2oniom

This program generates a Gaussian input file for ONIOM calculations from AMBER topology (.parm7) and restart (.rst7) files.

Available at: https://github.com/BILAB/pdb2oniom

PyHoleFinder

This program detects holes in images of the holey carbon films on a cryo-electron microscope (cryo-EM) grid. This program can work with SerialEM. With this program, detected holes can be grouped into 3×3 or 5×5 groups, which enables to efficiently acquire high-magnification images of 9 or 25 holes without moving the cryo-EM stage.

Available at: https://github.com/tterada-utokyo/PyHoleFinder

Biosynthetic Gene Cluster Database with Functional Annotations

This database provides plausible functional annotations of the genes in biosynthetic gene clusters based on the sequence similarity with functionally annotated proteins. The amino acid sequence of each gene product registered in the MIBiG (Minimum Information about Biosynthetic Gene) database was subjected to BLAST searches against the PDB and SwissProt sequence database. The results are stored in a relational database together with the functional annotation data provided by UniProt and the reaction data provided by Rhea. The user can search the database by MIBiG accession, protein ID, reaction participant name, or reaction participant substructre. This database helps the user to infer bound ligands and catalyzing reactions of a gene product and to find a gene product that is inferred to catalyze a reaction involving a given compound.

Server URL: http://sr.iu.a.u-tokyo.ac.jp/