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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• HTH3_numeration_assumed
• Molecular biology databases
• ETS numeration assumed

... Lathrop R.H., Rogers Jr R.G., Smith T.F. - A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment . ... Название: A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment . Авторы: Lathrop R.H., Rogers Jr R.G., Smith T.F. Аннотация: . A rigorous Bayesian analysis is presented that unifies protein sequence-structure alignment and recognition. ...

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• Heggins D., Taylor W. - Bioinformatics: Sequence, Structure and Databanks ::
• Peters C.A., Steenbrink J.H. - Mixed Hodge Structures :: Электронная библиотека

... If there's no significant multiple alignment , including the sequence, that you interest, then the secondary structure is built, using only the energy model (just the potential energy of the system is minimized), but very often such method will give unreliable results. ... It should be mentioned that by default, at alignment case, the RNA secondary structure will be predicted for the first sequence of the alignment. ... It is done through optimizing, not the real, but model energy of the structure. ...

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• Bioinformatics portal, Moscow State University
• OUTPUT
• Databases

... 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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• Align tool for DNA-protein complexes

DCSE . DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. ... It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system and checking of incorporated RNA structure. tkDCSE is a version of DCSE for X-Windows. ... Home Site: . ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - RnaViz

... Alternative core new atoms (%) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Geometrical core of a set of structures is a subset of alignment positions those atoms are disposed similarly in all structures. ... For any two positions included into geometrical core, the distances between CA atoms of those positions in all structures may differ not more than the value of the parameter "Distance spreading". ...

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• S : rm_systems
• Example of alignment

... 4 from monomer import AminoAcidType . ... 18 """ Sequence of Monomers . ... 21 * name -- str with the name of sequence . ... 26 * pdb_chains -- list of Bio.PDB.Chain's . ... 29 * pdb_residues -- dictionary like {Bio.PDB.Chain: {Monomer: Bio.PDB.Residue}} . ... 44 def __init__ ( self , monomers = None , name = '' , description = "" ): . ... 108 return Sequence ( monomers , name , description ) . ... 191 def pdb_has ( self , chain , monomer ): . ... 194 def secstr_has ( self , chain , monomer ): . ...

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• allpy: 675b402094be lib/sequence.py
• allpy: 835efa2a8c71 test/usecase1.py
• allpy: 6dfc736f37a9 lib/sequence.py

... Algorithm & . Format requirements . ... SDPsite is a tool for identification of protein active and other functional sites, based on spatial clustering of SDPs (specificity-determining positions, described here ) with CPs (conserved positions). ... Mapping predictied positions onto structure and construction of the best cluster . ... The input data of the algorithm are a multiple protein alignment divided into specificity groups . ... is called statistical significance of the set of k* positions . ...

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• Site Cluster
• SDPsite
• SDPsite - PF01205

... real.msf - выравнивание пространственных структур. Отмечено и цветом, и в строке Align, где выравниваются только два белка, где три, а где все четыре. script.src - скрипт для выделения области (не всей данной, потому что разобрать на общей все петли - тяжело) и раскрашивания разных цепей в разные цвета . ... A YGRWE- C YGQWE- D -GFWLE E GASFK- . ... 1 50 A AEIYNKDGNK LDVYGKVKAM HYMSDN.. ... 51 65 A ETQINDQLTG YGRWE C ETQINDQLTG YGQWE D TEDLGGGLKA GFWLE E SGTTDSGLEF GASFK Align ********** ***** . ...

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• Conservative Amino Acid Residues
• Summary Table Sequence
• Global and Local Alignment of A.A Sequences

This home page belongs to small group of scientists working at . Sternberg Astronomical Institute which is a part of Moscow State University . ... Электронная библиотека научно-технической и художественной литературы (доступна только из ГАИШ) . ... Local staff . Dr. Edward Kononovich (konon -at- sai.msu.ru), Associate Professor . ... Dr. Sergey Ayukov (asv -at- sai.msu.ru), Research Fellow, Webmaster of the group . ... Joint seminar of Solar Studies Structure Group and Solar Photometry Group . ...

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Anchoring patterns and point mutations in pairwise alignments using AlignMe X-ray crystal structures have revealed that numerous membrane proteins, such as GPCRs or some secondary transporters, despite the lack of any detectable sequence similarity between them, still share very similar 3D structures. ... The novel feature allows the user to define any number of anchors with varying strength for improving the quality of pairwise alignments in challenging cases lacking notable sequence similarity. ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/167.pdf

... Derived datatypes . Up: Point-to-Point Communication Next: Datatype constructors Previous: Null processes . ... Instead, MPI provides mechanisms to specify more general, mixed, and noncontiguous communication buffers. ... More general communication buffers are specified by replacing the basic datatypes that have been used so far with derived datatypes that are constructed from basic datatypes using the constructors described in this section. ... A sequence of basic datatypes . ... Центры . ...