dynamics.iam.u-tokyo.ac.jp

Laboratory of Computational Protein Science webservice page

Laboratory of Computational Protein Science. IMCB, The University of Tokyo. Web Service and Software Download. What does Dynomics do? 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). DTA DATABASE (Dihedral Transition Analysis database). Wataru Nishima, Guoying Qi, Steven Hayw...

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Laboratory of Computational Protein Science webservice page | dynamics.iam.u-tokyo.ac.jp Reviews

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Laboratory of Computational Protein Science. IMCB, The University of Tokyo. Web Service and Software Download. What does Dynomics do? 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). DTA DATABASE (Dihedral Transition Analysis database). Wataru Nishima, Guoying Qi, Steven Hayw...

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1 dynomics

2 pca nest

3 dta database

4 isa with sjade

5 scuba

6 cyclus

7 our group

8 reference

9 dta app

10 about us

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Laboratory of Computational Protein Science webservice page | dynamics.iam.u-tokyo.ac.jp Reviews

https://dynamics.iam.u-tokyo.ac.jp

Laboratory of Computational Protein Science. IMCB, The University of Tokyo. Web Service and Software Download. What does Dynomics do? 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). DTA DATABASE (Dihedral Transition Analysis database). Wataru Nishima, Guoying Qi, Steven Hayw...

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dynamics.iam.u-tokyo.ac.jp

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sjade

http://dynamics.iam.u-tokyo.ac.jp/ISA/sjade.html

Implementation of (S)JADE algorithm. Our implemenation of SJADE algorithm, which is used in our paper [1]. Users are strongly advised to read [2] and [3]. Users are required to provide one of BLAS-compatible libraries. I recommend Intel(R) MKL. Reference implementation of BLAS is not suitable because of its bad performance on modern CPUs. See README in the archive. This program does not have a fancy user interface; actually it's just a library, rather than a program. Dr Cardoso's JADE / BSS page.

2

uploader.html

http://dynamics.iam.u-tokyo.ac.jp/DTAapp

DTA app provides web interface of Dihedral Transition Analysis (DTA). From the two different structures in PDB format, DTA app automatically returns the result of DTA. The DTA is described in the original paper ( Bioinformatics 25(5), 628-635 2009. To understand how DTA app should work, please also take a look at DTA Database. And its description . Note the following algorithms of DTA app before uploading your own structures. Please upload two different structures in PDB format using following forms.

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Laboratory of Computational Protein Science

http://www.iam.u-tokyo.ac.jp/MolDes

Laboratory of Computational Protein Science. The University of Tokyo. Institute of Molecular Cellullar Biosciences. １１３００３２東京都文京区弥生１１１.

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Laboratory of Computational Protein Science webservice page

Laboratory of Computational Protein Science. IMCB, The University of Tokyo. Web Service and Software Download. What does Dynomics do? 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). DTA DATABASE (Dihedral Transition Analysis database). Wataru Nishima, Guoying Qi, Steven Hayw...

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