... 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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... Distances between sequences . It is considered that the space, where all amino acids and sequences are analysed, is a metric one. ... When the distance between amino acids is entered, it is rather easy to consider such measure as pair distance between sequences in any position of alignment (in fact, this distance is just a distance between two amino acids). As distance is an additional quantity, pair distance between sequences on all alignment positions can be easily defined. ...

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• About authors ot this complex
• About this project

... 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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• SDPlight

... 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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... 6 import sequence . ... 19 * self.alignment -- alignment object, which the block belongs to . ... 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 ): . ... 75 If more than one pdb chain for some sequence provided, consider all of them . ... 129 alignment_sequence = self . ... 136 def sequences_chains ( self ): . ...

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• allpy: fb3164f03984 lib/block.py
• allpy: b2ec17578145 lib/block.py
• allpy: 6dfc736f37a9 lib/block.py

... HELP ON SCREENING OF PATTERN OR ALIGNMENT AGAINST PROTEIN PROTEIN . ... The method of looking for all pattern entries (possibly inexact) in PROTEIN databank is almost the same as in PROSITE screening procedure. ... The screening by query alignment, based on the same principle: the alignment is seen as a pattern defining letter's frequencies in every position. The pattern example: . ... the only one capital letter at a position means that only given residue should be at the position. ...

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• RNA secondary structure prediction
• DIMACS Series in Discrete Mathematics
• BioSystems, 30 (1993) 57-63 57

... The standard IUPAC one-letter codes for the amino acids are used. ... Ambiguities are indicated by listing the acceptable amino acids for a given position, between square brackets `[ ]'. ... If your pattern consists of one-letter amino acid codes only, without any ambiguous residues, you need not specify the '-', i.e. you can directly copy/paste peptide sequences into the text field. ... To search all sequences which do not contain a certain amino acid, e.g Cys, you can use <{C}*>. ...

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• GeneBee service result

The method for homologous recombination detection within bacterial species Anastasia S. Kalinina1, Alexandra L. Suvorikova Vladimir G. Spokoiny 1 1,2,4 , 1,3,4 , Mikhail S. Gelfand 1,5 A.A. Kharkevich ... of sexual reproduction in bacteria, transfer of DNA fragments from cell to cell and introducing these fragments into a genome by homologous recombination plays a major role in spreading beneficial mutations through the population ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/244.pdf

... Next: It(Ut) tab (STM mode) Up: Scan parameters Previous: Plane tab Contents Index . On these tabs, similar by composition, user can set curves obtaining parameters for It(Z), F(Z) and D(Z) dependences: . ... N Scans -- Number of curves to be obtained. If some number is set in this field corresponding number of curves will be measured in forward and backward direction. ... Next: It(Ut) tab (STM mode) Up: Scan parameters Previous: Plane tab Contents Index Filonov 2005-02-04 ...

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• Sample landing preferences

fitcircle - find mean position and pole of best-fit great [or small] circle to points on a sphere. fitcircle [ xyfile ] -L norm [ -H [ nrec ] ] [ -S ] [ -V ] [ -: ] [ -bi [ s ][ n ] ] fitcircle reads lon,lat [or lat,lon] values from the first two columns on standard input [or xyfile ]. ... Then two locations are found: the mean of the input positions, and the pole to the great circle which best fits the input positions. ... If no file is specified, fitcircle will read from standard input. ...

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• Space position
• Galactic potential

... Along with the stable inner proton belt, temporal variations of the 1-15 MeV protons at L=2.5-3.5 have been reported, with intensity increases and decreases registered during and after strong magnetic storms. ... Our study presents experimental evidences that creation and destruction of solar proton belts in the inner magnetosphere may be produced by the fast shifts of the proton penetration boundary without additional acceleration and injection. ... Black line shows the 50-90 MeV proton profiles. ...

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GRS . GRS is a graphic tool for retrieval and visualization of genome segments from partially or completely sequenced genomes. To facilitate visual identification of conserved genomic motifs, genes are color-coded according to their presumed functional roles. ... The gene string analysis option of GRS allows the identification of genes that are identically arranged in any pairwise set of genomes. ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ...