Purpose of our Project

Protein structure modeling methods, such as homology modeling, protein-protein docking, and molecular dynamics (MD), have become important tools for drug target discovery. For routine tasks, such as building a single domain model from a closely homologous template, publicly available tools are sufficient. However, in the case of protein docking, even highly homologous complexes require sophisticated tools for model construction and refinement. The goal of this project is to make such sophisticated tools user friendly, even in the hands of non-experts. To achieve this goal we continuously collaborate with experimentalists in order to improve the accuracy and usability of our docking pipeline.


Software

 

 
Module Status Download
NMR Signal Assignment Module Under Construction Package Documentation
Restraints Generator Module Release 1 Package Documentation
Docking Module Release 1 Package Documentation
Clustering Module Release 1 Package Documentation
Filtering Module Release 1 Package Documentation
MD Calculation Module Release 1 Package Documentation
Scoring Module Release 1 Package Documentation
Supramolecule Extension Module Under Construction Package Documentation
Minimization Module Release 1 Package Documentation
 
 
We are also building a Docking Pipeline tool and the beta version is already up and running. It can be accesed here.
 
 
We present here an Artificial Neural Network (ANN) using novel fusion features for protein-RNA binding sites prediction, which is intended to serve as a better scoring function for protein-RNA docking MD... more
 

People

 



Daron M Standley
(Principal Investigator)
Associate Professor
iFReC


Kazutaka Katoh
(Collaborator)
Associate Professor
iFReC


Liang Shide
(Collaborator)
Assistant Professor
iFReC


Naohiro Kobayashi
(Collaborator)
Specially Appointed Researcher
Institute for Protein Research (IPR)


Songling Li
Post-Doctoral Fellow
iFReC


Joy Sarmiento
Software Engineer
iFReC


Tomoko Shimizu
Coordinator
iFReC

Contact

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4F IFReC Building, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871
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+81-6-6879-4264 (Phone)
+81-6-6879-4272 (Fax)