Laboratory of Computational Protein Science
IMCB, The University of Tokyo


Web Service and Software Download

Dynomics

What does Dynomics do?

Dynomics is an integral web services, providing experimentally characterized conformational changes (Dyndom)/dynamics as well as fast computations of the equilibrium dynamics based on theoretical models, derived from Elastic Network Models (GNM and ANM, in the residual level) for all the structures in Protein Data Bank. Also, for super biomolecules containing >9000 residues for GNM or > 1000 residues for ANM and small molecules < 300 residues for Normal Mode Analysis(in the atomic level), the dynamics results have been pre-calculated and stored in databases for instantaneous retrieval.

PCA_NEST

What does PCA_NEST do?

PCA_NEST calculates the Principal Components of any deposited NMR models in PDB. The NMR structure files, containing multiple models, should be submitted in PDB format. For retrieving pre-calculated PDB results go to the NMR_PCA database iPCA (more details).
Reference: Lee-Wei Yang, Eran Eyal, Ivet Bahar, and Akio Kitao, Principal Component Analysis of Native Ensembles of Biomolecular Structures (PCA_NEST): Insights into Functional Dynamics. Bioinformatics, 25, No.5, pp.606-614, Mar, 2009

DTA DATABASE (Dihedral Transition Analysis database)

DTA (Dihedral Transition Analysis) is the method to characterize the effects of large main-chain dihedral changes in protein. DTA DATABASE provides results of DTA from comprehensive and non-redundant dataset of 459 highresolution protein structure.
Reference: Wataru Nishima, Guoying Qi, Steven Hayward, and Akio Kitao, DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Bioinformatics, Vol. 25, No.5, pp.628-635, Mar, 2009

DTA app (Dihedral Transition Analysis application)

DTA app is a web application server of DTA (Dihedral Transition Analysis).
Reference: Wataru Nishima, Guoying Qi, Steven Hayward, and Akio Kitao, DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Bioinformatics, Vol. 25, No.5, pp.628-635, Mar, 2009

Independent Subspace Analysis (ISA) with SJADE

ISA (Indepedent Subspace Analysis) is the method to extract several independent subspaces in each of which collective modes are significantly correlated, and indentify the other modes as independent. ISA based on Subspace Joint Approximate Diagonalization of EIgenmatrices (SJADE) detects coupled collective motions in protein.
Reference: Shun Sakuraba, Yasumasa Joti, and Akio Kitao, Detecting coupled collective motions in protein by independent subspace analysis, J. Chem. Phys., 133, 185102 (2010); doi:10.1063/1.3498745

SCUBA

Molecular simulation software package, SCUBA (Simulation Codes for hUge Biomolecular Assembly) is now under development. This development has been being carried out as the collaboration with Quantum Bioinformatics Group and Computational Biology Group , Japan Atomic Energy Research Agency. SCUBA is an active software used in K computer.

CyClus

CyClus is a fast, comprehensive cylindrical interaface appoximation clustering/reranking method for rigid-body protein-protein dockin decoys. Now we are preparing for the first release.
Reference: Satoshi Omori & Akio Kitao, Proteins, Structure, Function and Bioinformatcs, in press, 2013. DOI: 10.1002/prot.24252.

 

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