. SDPpred: a tool for prediction of amino acid residues . that determine differences in functional specificity of homologous proteins .

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• SDPpred

... Many protein families contain homologous proteins that have a common biological function but different specificity. Given a multiple sequence alignment of a family divided into specificity groups, SDPpred predicts a set of alignment positions ( SDP, Specificity-Determining Positions ) that determine differences in the functional specificity. ... 2004) Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. ...

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• SDPsite - Algorithm Format requirements
• SDPlight

... 6 import sequence . ... 22 * self.positions -- list of positions of the alignment.body that . ... 25 Don't change self.sequences -- it may be a link to other block.sequences . ... 34 def __init__ ( self , alignment , sequences = None , positions = None ): . ... 44 self . ... 75 If more than one pdb chain for some sequence provided, consider all of them . ... 129 alignment_sequence = self . ... 130 return ( alignment_sequence [ i ] for i in self . ... 132 def ca_atoms ( self , sequence , pdb_chain ):...

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• allpy: 675b402094be lib/block.py
• allpy: 9adbec7c3366 lib/block.py
• allpy: 4f3d6b0af90b allpy/block.py

... 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
• SVETKA, a program for multiple sequence alignments analysis

... 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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... Values: 0 (Uncorrected); 1 (Jukes-Cantor); 2 (Kimura); 3 (Tamura); 4 (Tajima-Nei); 5 (Jin-Nei Gamma)) * -protmethod menu [0] Multiple substitution correction methods for proteins. ... Any integer value) * -calculatea boolean [N] This will force the calculation of parameter 'a' in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option). * -parametera float [1.0] User defined parameter 'a' to be use in the Jin-Nei Gamma distance calculation. ...

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• http://kodomo.cmm.msu.su/FBB/year_04/doc/BLAST_help/rpsblast.html
• http://kodomo.cmm.msu.ru/~ellys/blosum.html
• http://kodomo.cmm.msu.su/FBB/year_04/doc/BLAST_help/formatrpsdb.html

... 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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• Screening of pattern or alignment against PROTEIN databank
• AliComp - GeneBee Alignment Comparison Help
• BLAST Basic Overview

Positioning of Nucleosomes at DNA Containing Short Periodic Sequences A.P Lifanov1,3, V.J. Makeev1,2, N.G. Esipova 1 2 1 V.A. Engelhardt Institute of Molecular Biology, Moscow, Russia Vavilov Institute of General Genetics, Moscow, Russia 3 johnnie_me@list.ru Nucleosome distribution, alongside with histone modifications and RNA polymerase II (Pol II) occupancy shows preferential association with exons ( ... Histogram of relative positions of nucleosome and exon borders is shown in Fig. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/4.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/66.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/197.pdf

Evalign . Evalign is a computerised evaluation method for protein sequence alignment algorithm. It compares computer alignments with structural alignments of protein sequences and tells how correct your sequence alignment program is. It gives additional information on the characteristics of different alignment algorithms and shows types specific failings in alignment. ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - ClustalW
• Further Information and Bibliography
• SAL- Other Scientific Fields - Chemistry, Biology Related - SC_rate

Электронная библиотека Попечительского совета . ... Althaus E. - A branch-and-cut algorithm for multiple sequence alignment . ... Название: A branch-and-cut algorithm for multiple sequence alignment . Автор: Althaus E. Язык: . ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Walrath K., Campione M., Huml A. - JFC Swing Tutorial, The: A Guide to
• Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the
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... 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 . ...

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• Pack and unpack | PARALLEL.RU - Информационно-аналитический центр по
• Data Access Routines | PARALLEL.RU - Информационно-аналитический центр по

... To run the <LAYER> version of the example, select: flower.htm . ... However, if the page had several layers with absolute positions, and you wanted to place another layer in a relative position to one of the existing layers, you could use inline JavaScript to calculate the value for LEFT or TOP . ... In this example, there is really no need to use inline JavaScript to position the last flower layer, since you could just let the TOP value default to its natural value, as in the other flower layers. ...

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• Long description illustrating absolute positioning with respect to the initial
• Long description of example illustrating table row height calculations and
• Long description for example illustrating positioning with respect to a

... MATHEMATICAL AND SYSTEM BIOLOGY UDC 577.1 Membrane Profile-Based Probabilistic Method for Predicting Transmembrane Segments via Multiple Protein Sequence Alignment R. A. Sutormina and A. A. Mironova a b , b, c State Research Center GosNIIgenetika, Moscow, 117545 Russia; e-mail: sutor_ra@mail ... Bioinformatics, Moscow State University, Moscow, 119992 Russia Received January 25, 2006 Abstract--Prediction of transmembrane (TM) segments of amino ... Protein Sci. ... Proteins. ...

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• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2014.pdf
• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2013.pdf
• http://storage.bioinf.fbb.msu.ru/~roman/batmas30.pdf

... Investigations of the electrical properties of PbSnTeS, PbSnTeSe, and PbSnSeS solid solutions confirmed an earlier hypothesis that the positions of the tin atoms were off-center and that the tunnel motion of these atoms were suppressed in the anion sublattice. ... Other works on off-center impurities ...

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... This page is a reference for all CSS classes used in PatternSkin . ... All templates that are not the view template have the body class name "patternNoViewPage". ... Search results .patternSearchResults - container on rename pages (no longer used on actual search results 'view' pages) .patternSearchResultsHeader - horizontal bar with the web color .patternSearchResults - block of one result .patternSearchResultCount - the number of results .patternSearched - feedback on the string used to search . ...

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• PatternSkinCss - TWiki - TWiki - (printable)
• Simple calendar setup [flat calendar]
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Construction of sequences of zeros and ones with complex finite sequences / A. Yu. ... Vestnik Moskovskogo Universiteta. Seriya 1. ... We construct infinite sequences of zeros and ones under some restrictions (not to contain subwords of some definite type or definite bits at definite positions, etc.) This paper concerns probabilistic methods of constructing such sequences with application of Lov sz lemma and their reformulation in terms of the Kolmogorov complexity and Martin-L f randomness. ...

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Home . Database of structures of nucleic acid - protein complexes . ... List of complexes . Pfam families . SCOP families . Interaction classes . ... NPIDB . ... Information on SCOP and Pfam domains detected in protein chains is presented. ... Each family has its own web page with the list of entries that include domains of the family. ... List of SCOP domains occurred in DNA-protein and RNA-protein complexes is organized in tree-like form, according to the SCOP classification. ...

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... It interpolates the grid at the positions in the table and writes out the table with the interpolated values added as a new column. A bicubic [Default] or bilinear [ -Q ] interpolation is used, requiring boundary conditions at the limits of the region (see -L flag option). xyfile This is an ASCII [or binary, see -b ] file where the first 2 columns hold the (x,y) positions where the user wants to sample the 2-D data set. ... Default is 2 input columns]. -bo Selects binary output. ...

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• http://xray.sai.msu.ru/~ivan/gmt/man/fitcircle.html
• AXAF-Chandra
• Space position

This section contains information of how user agents should treat control characters and other special characters. ... There are 256 character positions in the Latin-1 encoding. ... It consists of the space character, 186 characters that form a subset of the graphic characters in ISO 6937/2 (1983), and four additional characters that are intended for inclusion in ISO 6937/2. ... Certain characters are taken to have special meaning within the context of an HTML document. ...

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• Table Rows
• Passing arguments to the shell
• Divisions

You are here: Foswiki > System Web > Skins > PatternSkin > PatternSkinCss (revision 1) E dit A ttach . This page is a reference for all CSS classes used in PatternSkin . ... colors.css : text colors, background colors, border colors . ... Positional containers are referred by id, for instance #patternSideBar . ... patternScreen - outer container, used when centering the page (see PatternSkinCssCookbookCenterPage ) . ... patternTopBarContents - header art / logo; contains topic WebTopBar . ...

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• JQueryMasonry < System < Foswiki