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Bio-Knowledge Engineering Research Laboratory

Bioinformatics Center, Institute for Chemical Research, Kyoto University
Gokasho, Uji, Kyoto 611-0011, Japan
Phone: +81-774-38-3023
Fax: +81-774-38-3037

https://www.bic.kyoto-u.ac.jp/pathway/

Software developed

Here is a sort of web pages of software we have developed. Sorted, roughly according to the years most relevant papers published. Enjoy!

Graph network simulation for biomaterials (preliminary work)

Data, results and codes, ChemRxiv 2023 [DOI], ACS Biomaterials Science & Engineering 2024 [DOI]

Copolymerization database

CoPolDB, ChemRxiv 2023 [DOI], Polymer Chemistry 2024 [DOI]

Predicting drug-drug interactions

SPARSE, ISMB 2022 [DOI]

Metabolite identification

ADAPTIVE, ISMB 2019 [DOI]
SIMPLE, ISMB 2018 [DOI]

Protein function prediction

NetGO (Web server), Nucleic Acids Research 2019 [DOI]

Weighing edges in graph

AEW, NeurIPS 2013 [Paper site], Machine Learning 2017 [DOI]

Integrating multiple graphs

SMGI, IEEE TNNLS 2013 [DOI]

Finding repeats

RRS, Discrete Applied Mathematics 2013 [DOI]

Metabolic pathway mining

NetPathMiner, Bioinformatics 2014 [DOI]
PathRanker R Package, WABI 2009 [DOI], Bioinformatics 2010 [DOI]

Calpain cleavage site prediction

CaMPDB (Database + web service), IBSB 2009 [DOI], Plos One 2013 [DOI], Molecular & Cellular Proteomics 2016 [DOI], MiMB 2019 [DOI]

Biomedical text mining

PURE, IBSB 2007 [DOI]

Glycome informatics

ProfilePSTMM (Web service), ISMB 2006 [DOI]
KCaM (Web service), Nucleic Acids Research 2004 [DOI]

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