dpidb.genebee.msu.ru

S&S

The page of the interdisciplinary seminar/working group based on the Department of Mathematical Methods in Biology. Of AN Belozersky Institute. In investigations of biological features and 'living systems' we try to follow the approaches of Izrael Gelfand, the organizer of the Department. 151; a database of structures of DNA-protein and RNA-protein complexes. Old version of NPIDB. 151; a probe-level annotation database for Affymetrix expression microarrays. Genome assembly and annotation. 151; structural...

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<META> DESCRIPTION

The page of the interdisciplinary seminar/working group based on the Department of Mathematical Methods in Biology. Of AN Belozersky Institute. In investigations of biological features and 'living systems' we try to follow the approaches of Izrael Gelfand, the organizer of the Department. 151; a database of structures of DNA-protein and RNA-protein complexes. Old version of NPIDB. 151; a probe-level annotation database for Affymetrix expression microarrays. Genome assembly and annotation. 151; structural...

<META> KEYWORDS

1 structures and sequences

2 moscow state university

3 our projects

4 data base

5 npidb

6 plandbaffy

7 tools

8 clud

9 conclus

10 svetka

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structures and sequences,moscow state university,our projects,data base,npidb,plandbaffy,tools,clud,conclus,svetka,nhunt,npg explorer,plot hits,wlake,malakite,blocks 3d/pair cores,proton,architectures,and structural motifs,gcore,lcore,structalign,mtpro

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S&S | dpidb.genebee.msu.ru Reviews

https://dpidb.genebee.msu.ru

The page of the interdisciplinary seminar/working group based on the Department of Mathematical Methods in Biology. Of AN Belozersky Institute. In investigations of biological features and 'living systems' we try to follow the approaches of Izrael Gelfand, the organizer of the Department. 151; a database of structures of DNA-protein and RNA-protein complexes. Old version of NPIDB. 151; a probe-level annotation database for Affymetrix expression microarrays. Genome assembly and annotation. 151; structural...

INTERNAL PAGES

dpidb.genebee.msu.ru

1

ArchiP homepage

http://www.dpidb.genebee.msu.ru/archip

Roteins (ver. beta.1603061903). Of all-β and α/β-classes. Older version of ArchiP is available. Outline of ArchiP algorithm: 1. Protein structure in PDB format and β-sheet maps. And boudaries of α-helixes are taken as input.2. β-barrels, contacts between β-sheets and between β-sheets and layers of α-helixes are detected. 3. Architectuires. Are detected as a sets of contacted units (β-sheets, β-barrels and/or layers of α-helixes). Start new ArchiP job. Regions of β-sheets.

2

SheeP homepage

http://www.dpidb.genebee.msu.ru/sheep

Uzzle (ver. beta.1603061903). SheeP displays schemes of β-sheet called draws β-sheet maps. Older version of SheeP is available. Outline of SheeP algorithm: 1. Protein structure in PDB format is taken as input. 2. Secondary structures are detected. 3. β-sheet maps. Are created. 4. Maps are modified. Start new SheeP job. Show sheet maps help. Location (up or down the sheet). Beta;-strands and α-helixes.

3

S&S: Projects

http://www.dpidb.genebee.msu.ru/projects.html

List of 3D structures of components of restriction-modification systems with links to NPIDB. Comparison of protein phylogeny reconstruction methods. Nhunt, a program for similarity search of nucleic sequences. Results on genome word compositions and contexts of mutations. Bacterial secretion systems of type III.

4

MotAn homepage

http://www.dpidb.genebee.msu.ru/motan

Alyzer (ver. beta.1603061903). MotAn detects structural motifs. Older version of MotAn is available. Outline of MotAn algorithm: 1. Protein structure in PDB format and β-sheet maps. And boudaries of α-helixes are taken as input.2. Structural motifs. Start new MotAn job. Beta;-strands and α-helixes. Please, cite: Aksianov E. Motif Analyzer for Protein 3D Structures. J. Struct. Biol. Work on this service is supported by Russian Foundation of Basic Research, grants 13-07-00969 and 14-04-31709 mol a.

5

S&S: Protein families

http://www.dpidb.genebee.msu.ru/families.html

Protein families studied by our group. Lambda repressor-like family of DNA-binding domains. Cro/C1-type HTH domains, HTH 3). LAGLIDADG homing endonucleases (all Pfam families). Intein-encoded LAGLIDADG homing endonucleases. Restriction endonucleases of type II.

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The page of the interdisciplinary seminar/working group based on the Department of Mathematical Methods in Biology. Of AN Belozersky Institute. In investigations of biological features and 'living systems' we try to follow the approaches of Izrael Gelfand, the organizer of the Department. 151; a database of structures of DNA-protein and RNA-protein complexes. Old version of NPIDB. 151; a probe-level annotation database for Affymetrix expression microarrays. Genome assembly and annotation. 151; structural...

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