... optimization of rasmol_homology: keep structure loaded of two sequences only One of steps of this program is superimposition of all sequences with main sequence and saving of all structures to pdb file. ... To implement this optimization methods supeimpose and save_pdb of alignment were replaced with methods with same names of sequence. ... Markup ): . ... 6 def from_record ( cls , container , record , name = None ): . ... 17 def to_record ( self ): . ... 30 for number , monomer in enumerate ( self ...

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• allpy: d137df18a8bf allpy/markups.py
• allpy: 3a712982ceb8 allpy/markups.py
• allpy: 116f5bfc39b8 allpy/markups.py

... List of solitary restriction endonucleases in complete prokaryotic genomes . List of groups of orthologous R-M systems. List of all analyzed genomes. Contains those orthologous groups that include at least one separated R-M system . R-M orthologous group ID . REs alignments . MTases alignment . Group 1 . ...

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• Geometrical core

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
• ETS numeration assumed
• ETS_all_contacts alignment

... 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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• SDPsite - PF07978
• SDPsite - PF01399
• SDPsite - PF01139

S .. ... SNP regions in the dataset are 21bp fragments of the genome containing SNP in the middle position . ... Word frequencies in SNP regions of the human genome (zip file, 66 MB) . ... Word frequencies in SNP regions of the human genome (xls file, 1.2 MB) . The file contains the frequency of each word of length 1, 2, 3, 4 or 5 in flanks of SNP regions for several criteria of SNP selection. These frequencies are compared to the frequencies of the same words in the complete human genome . ...

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• ConClus

... Sinergetic has recommended itself in the most various areas: to physics, chemistry, biology, and even in public sciences. ... The purpose of research was the study of laws of heat transfer process in active environment, which is nonequilibrium and itself can give the contribution to change of temperature. ...

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... Structure and properties of chimeric small heat shock proteins containing yellow fluorescent protein attached to their C-terminal ends. ... Recombinant chimeras of small heat shock proteins (sHsp) HspB1, HspB5, and HspB6 containing enhanced yellow fluorescent protein (EYFP) attached to their C-terminal ends were constructed and purified. Some properties of these chimeras were compared with the corresponding properties of the same chimeras containing EYFP attached to the N-terminal end of sHsp. ...

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• The role of intrinsically disordered regions in the structure and functioning
• Structure, properties, and functions of the human small heat-shock protein
• Effect of mutations in the beta5-beta7 loop on the structure and properties of

... The LanHEP input file is the sequence of statements, each starts with a special identifier (such as parameter, lterm etc) and ends with the full-stop ' . ... This section is aimed to clarify the syntax of LanHEP input files, i.e. the structure of the statements. ... Let us consider the LanHEP input files for the Standard Model with both the t'Hooft-Feynman and unitary gauges. ... LanHEP allows the user to define several keys , and use these keys to branch among several variants of the model. ...

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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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• Partitioning of Cartesian structures | PARALLEL.RU -

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/17.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/42.pdf

... Hexameric AAA+ ATPases induce conformational changes in a variety of macromolecules. AAA+ structures contain the nucleotide-binding P-loop with the Walker A sequence motif: GxxGxGK(T/S). A subfamily of AAA+ sequences contains Asn in the Walker A motif instead of Thr or Ser. ... To determine functional effects of introduction of Asn into the Walker A sequence, we replaced the Walker-A Thr with Asn in ClpB, a bacterial AAA+ chaperone which reactivates aggregated proteins. ...

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• http://kodomo.cmm.msu.ru/~igogo/Term3/uni.txt
• статьи о карбоксилэстеразе bioH
• UniProt fields

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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• Not so well documented Device Helpers in OS/2

... LDAP is the Lightweight Directory Access Protocol, and is a protocol used to access "Directory Servers". ... Search surname entry $sr= ldap _ search ($ds, o=My Company, c=US , sn=S* ); echo Search result is .$sr. p ; echo Number of entires returned is . ldap _count_ entries ($ds,$sr). p ; echo Getting entries ... p ; $info = ldap _ get _ entries ($ds, $sr); ... ldap_get_attributes -- Get attributes from a search result entry . ... ldap_get_entries -- Get all result entries...

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• mcal_fetch_current_stream_event
• xml_parse_into_struct
• Strings

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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• NPIDB: 5DPK structure

Электронная библиотека Попечительского совета . ... Heggins D., Taylor W. - Bioinformatics: Sequence, Structure and Databanks . ... Название: Bioinformatics: Sequence, Structure and Databanks . Авторы: Heggins D., Taylor W. Аннотация: . Bioinformatics covers practical important topics in the analysis of protein sequences and structures. ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Lathrop R.H., Rogers Jr R.G., Smith T.F. - A Bayes-optimal sequence-structure
• Zung N.T. - Poisson Structures and their Normal Forms :: Электронная библиотека
• 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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• Databases
• Screening protein sequence against PROSITE databank
• GeneBee service

A.V. Churakov, L.G. Kuz'mina, D.A. Lemenovskii . J.Organomet.Chem., v. 485, p. C81-C83 (1995) . ABSTRACT . The possibilities of functionalization Cp-ligands in p-complexes Ti, Zr and Hf are examined. Laboratory of Coordination Organometallic Compounds

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• Colloid-chemical phenomena in wastewater containing lignosulphonates
• Synthesis and Crystal Structure of Nitratocuprates(II) of Alkaline Metals and
• New titanium and zirconium sandwich and half-sandwich complexes containing the

. The UNIX file system is organised as a hierarchy of directories starting from a single directory called root which is represented by a / (slash). Imagine it as being similar to the root system of a plant or as an inverted tree structure. Immediately below the root directory are several system directories that contain information required by the operating system. The file holding the UNIX kernel is also here. UNIX system directories . Home directory . Pathnames .

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• Directories
• The Structure of HTML 3.0 Documents
• About the Concepts menu

RNA Tertiary Structure Modelling . ... Two steps to fold coarse-grained model of RNA tertiary structure . ... fill in RNA secondary structure form with CT format (also with pseudoknots); . ... push "Finish Step #1" button to obtain secondary and intermediate* structures. * intermediate structure is the structure with minimum of "free energy" contains formed helixes and stacking, but without tertiary interactions . RNA secondary structure form . ... some useful RNA secondary structure databases: . ...

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• TWikiMetaData - TWiki - TWiki - (printable)

A collection class is a class that can contain a number of items in a certain data structure and perform operations on the contained items; insert, remove, find etc. ... QList ; a doubly linked list structure. ... An iterator is a class for safely traversing the items in a collection: . ... Qt has an array template class, QArray , which stores the items directly in the array. ... We discuss QList here, but the same applies for all collection classes and all collection class iterators. ... Classes: . ...

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• Unknown Constructed Types
• Qt Toolkit - QKeyEvent Class