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1. About
. A program for alignment of structures of DNA-protein complexes . Home . Feedback . Help . About . StructAlign v1.0 is developed and maintained by a team from A.N. Belozersky Institute of Physico-Chemical Biology MSU and Faculty of Bioengineering and Bioinformatics MSU. You can read more in: Biochemistry (Moscow), 2015, Vol. 80, No. 11, pp. 1465-1468 (DOI: 10.1134/S0006297915110073) .
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Ссылки http://mouse.genebee.msu.ru/tools/StructAlign/StructAlign_about.html -- 3.4 Кб -- 14.03.2016
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2. Align tool for DNA-protein complexes
. A program for alignment of structures of DNA-protein complexes . Home . Feedback . Help . About . Input PDB code of the first complex: and chain of the protein (optional): . Input PDB code of the second complex: and chain of the protein (optional): . If you get stuck with program input, try example data and click Align! Example data . 2016
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Ссылки http://mouse.genebee.msu.ru/tools/StructAlign.html -- 5.0 Кб -- 03.03.2016
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3. S publications
Ledneva R.K., Alekseevskii A.V., Vasil'ev S.A., Spirin S.A., Kariagina A.S. Structural aspects of interaction of homeodomains with DNA . Molecular Biology (Moscow) 2001, 35 (5):647?659 [ SpringerLink ] . ... Anna S. KARYAGINA, Andrei V. ALEXEEVSKI, Andrei V. GOLOVIN, Sergei A. SPIRIN, Olga V. VOROB'EVA, Elena A. KUBAREVA. ... Biophysics (Moscow) , vol. ... Ershova A.S., Alexeevski A.V., Spirin S.A., Karyagina A.S. Common structural features of homeodomains and homeodomain-DNA complexes. ...
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Ссылки http://mouse.genebee.msu.ru/publications.html -- 10.5 Кб -- 11.01.2016
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4. Nhunt
... Pairwise Tabular Tabular with headers . E-value threshold . Diagonal threshold . ... Escherichia coli str. ... W3110 Yersinia pestis KIM10+ Mycobacterium tuberculosis CDC1551 Bacillus subtilis subsp. subtilis str. ... Algorithm: Sergei Spirin, Yury Pekov . Programming: Yury Pekov . ... Funding: Ministry of Education and Science of the Russian Federation, State Contract No. 07.514.11.4006 (algorithm) . Russian Foundation for Basic Research, grant no. 13 07 00969 (web interface). ...
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Ссылки http://mouse.genebee.msu.ru/tools/nhunt.html -- 5.8 Кб -- 23.12.2015
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5. http://mouse.genebee.msu.ru/tools/nhunt_example.fasta
>valV gcgttcatagctcagttggttagagcaccaccttgacatggtgggggtcg ttggttcgagtccaattgaacgcacca
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Ссылки http://mouse.genebee.msu.ru/tools/nhunt_example.fasta -- 1.1 Кб -- 23.12.2015
[ Сохраненная копия ] Ссылки http://mouse.genebee.msu.ru/~bennigsen/nhunt_example.fasta -- 1.1 Кб -- 26.03.2012
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[ Сохраненная копия ] Ссылки http://mouse.genebee.msu.ru/~bennigsen/nhunt_example.fasta -- 1.1 Кб -- 26.03.2012
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6. Nhunt
Threshold of e-value . Diagonal threshold . ... Escherichia coli str. ... W3110 Yersinia pestis KIM10+ Mycobacterium tuberculosis CDC1551 Bacillus subtilis subsp. subtilis str. 168 Archaeoglobus fulgidus DSM 4304 Sulfolobus solfataricus P2 Mus_musculus.GRCm38.69 Caenorhabditis_elegans.WS220.69 Homo_sapiens.GRCh37.69 Callithrix_jacchus.C_jacchus3 Algorithm: Sergei Spirin, Yury Pekov . Programming: Yury Pekov . ... 07.514.11.4006) . S 2012-2015 ...
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Ссылки http://mouse.genebee.msu.ru/~bennigsen/nhunt_interface.html -- 4.7 Кб -- 17.12.2015
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7. LCore
. LCore is a program for classification of 3D structures of macromolecular complexes on the basis of their geometric core. Distance threshold (?) . Minimal core size (#aa's) . Alternative core new atoms (%) . Max number of cores on output . Core identifier for chain superimposition (0 for the main core) .
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Ссылки http://mouse.genebee.msu.ru/tools/life_core.html -- 2.7 Кб -- 28.10.2015
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8. StructAlign feedback
. A program for alignment of structures of DNA-protein complexes . Home . Feedback . Help . About . If you have some questions or you have found an error, send us a letter using this form: . Your name: . Your e-mail: . Message: .
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Ссылки http://mouse.genebee.msu.ru/tools/StructAlign/StructAlign_feedback.html -- 3.3 Кб -- 23.10.2015
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9. StructAlign help
A program for alignment of structures of DNA-protein complexes . ... Help . ... StructAlign is a program for alignment of DNA-protein complexes' structures. The program gets a pair of complexes of DNA double helix with proteins in PDB-format and optionaly names of protein chains and outputs an alignment of DNA chains corresponding to the best spatial fit of protein chains also in PDB-format. ... X-axis is directed from P atom to C1' atom. ...
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Ссылки http://mouse.genebee.msu.ru/tools/StructAlign/StructAlign_help.html -- 5.2 Кб -- 23.10.2015
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10. S
S .. ... a database of structures of DNA-protein and RNA-protein complexes. ... a program for finding hydrophobic clusters in 3D structures of macromolecules . ... search of conserved hydrophobic clusters in aligned 3D structures of protein families . ... a program for analysis of multiple alignments . ... a program for automatic detection of aligned blocks in a multiple protein alignment. ... a program for detection of aligned blocks in a multiple alignment of sequences of PDB chains. ...
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Ссылки http://mouse.genebee.msu.ru/ -- 7.7 Кб -- 02.10.2015
[ Сохраненная копия ] Ссылки http://mouse.genebee.msu.ru/index.html -- 7.7 Кб -- 02.10.2015
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[ Сохраненная копия ] Ссылки http://mouse.genebee.msu.ru/index.html -- 7.7 Кб -- 02.10.2015
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11. Example of alignment
Here are examples of an alignment for input for the program " LCore ". ... 1NK2 (TGTGTCAAGTGGCTGT):A.P/1 (ACAGCCACTTGACACA):B.P/1 (ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP):P.CA/1 1NK2 (TGTGTCAAGTGGCTGT):A.P/2 (ACAGCCACTTGACACA):B.P/2 (ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP):P.CA/2 1NK2 (TGTGTCAAGTGGCTGT):A.P/3 (ACAGCCACTTGACACA):B.P/3 (ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP):P.CA/3 ...
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Ссылки http://mouse.genebee.msu.ru/tools/LCexample.html -- 2.3 Кб -- 20.06.2015
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12. ConClus
... Minimal size of Clud clusters (residues) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Hydrophobic cluster of a single protein structure is a separated pool of nonpolar atoms. Usually there is the biggest cluster in the protein called hydrophobic core. ... ConClus program is able to detect of conservative hydrophobic clusters for a family of related protein domains or just for a set of aligned proteins. ...
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Ссылки http://mouse.genebee.msu.ru/~bennigsen/conclus.html -- 3.9 Кб -- 13.05.2015
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13. S : Protein families
. Homeodomains . Lambda repressor-like family of DNA-binding domains (Cro/C1-type HTH domains, HTH_3) . ETS domains . LAGLIDADG homing endonucleases (all Pfam families) . Intein-encoded LAGLIDADG homing endonucleases . Restriction endonucleases of type II (in Russian) . PorB (in Russian) . Zinc fingers C2H2 (in Russian) . DNA methyltransferases
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Ссылки http://mouse.genebee.msu.ru/families.html -- 2.2 Кб -- 28.01.2015
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14. S : Projects
. Restriction-modification systems . 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 Under construction
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Ссылки http://mouse.genebee.msu.ru/projects.html -- 2.9 Кб -- 28.01.2015
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15. Molecular biology databases
... Protein sequences . ... European ribosomal RNA database . ... Thermodynamic database for protein-nucleic acids interactions (Japan) . ... Families of structurally similar proteins . ... Database of protein families and HMMs (collection of multiple sequence alignments and hidden Markov models) . ... Collection of protein families constructed by clustering complete protein sequences. ... Database issues of NAR: vol. 31 (2003) , vol. 32 (2004) , vol. 33 (2005) , vol. 34 (2006) , vol. 35 (2007) , vol. ...
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Ссылки http://mouse.genebee.msu.ru/NPIDB/mbdb.html -- 8.5 Кб -- 21.04.2014
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16. http://mouse.genebee.msu.ru/biofizika/clud_draft.pdf
CluD, a Program for the Determination of Hydrophobic Clusters in 3D Structures of Protein and Protein-Nucleic Acids Complexes Andrei ALEXEEVSKI, Sergei SPIRIN, Daniil ALEXEEVSKI, Oleg KLYCHNIKOV, Anna ERSHOVA1 ... .ru 1 Institute of Agricultural Biotechnology, Timiryazevskaja street, 42, Moscow, 127550, Russia; anna@iab.ac.ru Annotation In structures of macromolecules, hydrophobic clusters are spatial areas filled mainly by non-polar atom groups ...
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Ссылки http://mouse.genebee.msu.ru/biofizika/clud_draft.pdf -- 818.2 Кб -- 11.04.2014
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17. PLANdbAffy main
. Description . Annotation database for human . Annotation database for mouse . Annotation database for rat Partially suppurted by RFBR grant 10-07-00685-а . Ramil Nurtdinov
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Ссылки http://mouse.genebee.msu.ru/PLANdbAffy/index.html -- 1.9 Кб -- 10.01.2013
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18. Nhunt: program for nucleic acid sequence similarity search
. Nhunt: program for nucleic acid sequence similarity search . Download . User manual . Application examples . License . News . About . Authors publications . Contacts . Web interface . At present you can download poster from MCCMB'11 conference and my term work (in Russian) with description of main program algorithms. Funding: Ministry of Education and Science of the Russian Federation (State Contract No. 07.514.11.4006). Copyright 2010-2011 Yury Pekov
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Ссылки http://mouse.genebee.msu.ru/~bennigsen/nhunt_files/about.html -- 5.3 Кб -- 28.11.2012
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19. Nhunt: program for nucleic acid sequence similarity search
... Instructions are in README.TXT file inside the tarball. ... tar -xvf nhunt_x86.tar Query and database files should contain sequences in FASTA format ( wikipedia description ). ... Default name of the output file is 'nhunt.out'. ... Any parameter consists of key and value and is called as '-key value', where 'key' is one character and 'value' is any number of characters. -i Query file . ... No default value. -d Database file . ... No default value. -o Output file . ... Default value: 'nhunt.out' . ...
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Ссылки http://mouse.genebee.msu.ru/~bennigsen/nhunt_files/manual.html -- 9.0 Кб -- 26.09.2012
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20. Nhunt: program for nucleic acid sequence similarity search
... License . ... This program is free software: you can redistribute it and/or modify . it under the terms of the GNU General Public License as published by . the Free Software Foundation, either version 3 of the License, or . ... This program is distributed in the hope that it will be useful, . ... GNU General Public License GNU General Public License for more details. ...
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Ссылки http://mouse.genebee.msu.ru/~bennigsen/nhunt_files/license.html -- 5.5 Кб -- 26.09.2012
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