... annotate . ... Please note that `Sequence` API almost changed entirely! ... dendik@1076 . ... 8 * greatly improved markups support and markups IO . ... 12 * and a lot of work on ` blocks3d ` and ` pair_cores ` with many new features , . ... 39 * new : added ` MarkupIOMixin ` which simplifies defining savable markup classes . ... 40 * new : added pre - defined generic markups for simple data types ( int , char , . ... 68 * new : Alignments , Sequences and Blocks now can have Markups , see the wiki . ...

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• allpy: 2b3cad50c2b1 NEWS

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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• ETS_all_contacts alignment

... 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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• PLANdbAffy: probe-level annotation database for Affymetrix expression
• S : rm_systems
• Example of alignment

... 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 ::
• Jensen K.V. - The Ni-YSZ interface. Structure, composition and electrochemical
• Widom B. - Structure of Interfaces from Uniformity of the Chemical Potential ::

... 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
• Genebee Predicted Annotation - Advanced
• Bioinformatics portal, Moscow State University

... Query: E. coli K12 tRNA (valV, selC, asnV, leuT, argZ from EMBL entry U00096 ) . ... BLASTN (both) | ... Nhunt . ... BLASTN (optimal): 3.5 s . BLASTN (default): 0.8 s . ... Nhunt: 7 s The program Nhunt surpass all other tested programs in sensitivity. ... Nhunt BLASTN (optimal): 2.9 s . ... Nhunt: 3.7 s BLASTN with default parameters actually cannot find any significant homologues. ... Nhunt-3: 1.7 s BLASTN with default parameters actually cann't find any significant homologues. ...

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• ConClus
• 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
• SAL- Other Scientific Fields - Chemistry, Biology Related - Protein Structure
• Zen: UserCatalogs

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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• Work notes

Sequence alignment of non-superposable beta-sheets Evgeniy Aksianov Belozersky Institute, Lomonosov Moscow State University, Leninskie Gori 1, Moscow, Russia, evaksianov@gmail.com Andrey V. Alexeevski Belozersky Institute, Lomonosov Moscow State University, Scientific Research Institute for System Studies (NIISI RAN), Moscow, Russia aba@belozersky.msu.ru Protein 3D structures usually are more conserved than their sequences. ... Beta-strands are contained in sheet map rows. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/18.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/4.pdf

... 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
• Site Cluster
• SDPlight

Key-words: rhythm, stress, syllable, rhythmic structure, syntagm, utterance, prosody, speech production, speech perception . ... In speech communication, RS are both units of speech production and speech perception. ... The research of speech rhythm in diachrony and synchrony consists of the analysis and the description of speech rhythmic units concerning Old Church Slavonic, Old Russian, Old High German in diachrony and Modern Russian, German, Czech and Bulgarian in synchrony. ...

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. Color Explanation . Red absolutely conservative a.a residues (i.e. 100% identity) . 80% identity . 60% identity . No color . Percentage of Conservative Residues within the Ligand Contact Area . 25/34 = 0.735 . Santesson Elly, 2004

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• Structure Alignment
• Summary Table Sequence
• Task 9 (sequence annotation)

SCIENTIFIC TASKS AND RESULTS . In the results of searching for new perspective solid state materials for the quantum electronics, non-linear optics and other fields of physics more than 200 various oxide compounds were synthesized and peculiarities of their atomic structure and physical properties are studied. Single crystals of 80 such the compounds are grown and thoroughly investigated. ... A family of oxide-ion conductors on the base of La 2 Mo 2 O 9 (30.10.09) . ... Main page ...

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• Sequence Design of Copolymers with Special Functional Properties - Chair of
• Selected publications of Ivanov, Viktor Alexandrovich

download:rn-031116 ]] . CompHEP . ... Documentation and help files . ... New scheme of work with initial beams and final composite particles was changed. If you have a private model and want to use them with CompHEP-4.4.0, you have to copy cpart1.mdl file to cpartN.mdl file where N is a number of your model by commands: cd path_to_user_working_directory/model cp cpart1.mdl cpartN.mdl . All new composite particles must be introduce into table by using edit model facilities. ... Downloads . ...

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• overview [CompHEP]

... 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_event_add_attribute
• Alternative syntax for control structures

... Next: DSP board program Up: SPM Installation Previous: Mechanical system of the Contents Index . Figure 1.3: Software structure. The server part of the software is working under Windows NT or XP operating systems. ... Second level - operating system driver, that allow to exchange data with DSP board through input/output ports. ... This structure is a result of qualities this system should satisfy: precise process synchronization, hi-speed data transfer, network support, convenience in usage. ...

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• FemtoScan Online program

Next: Subtyping Up: Untyped values Previous: Untyped values . ... 1: // IDL 2: struct foo { 3: long l; 4: short s; 5: }; 6: 7: // C++ 8: void operator<<= ( CORBA::Any &a, const foo &s ) 9: { 10: a.type( _tc_foo ); 11: a.struct_put_begin(); 12: a <<= s.l; 13: a <<= s.s; 14: a.struct_put_end(); 15: } 16: 17: CORBA::Boolean operator>>=( const CORBA::Any &a, foo &s ) 18: { 19: return a.struct_get_begin() && 20: (a >>= s.l) && 21: (a >>= s.s) && 22: a.struct_get_end(); 23: } . ...

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• Modules
• Implementation Repository
• A generic DII interface

... 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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• General structure
• Graphical interface
• Contents

Structure of the Chemistry Department . ANALYTICAL CHEMISTRY DIVISION . LABORATORY OF KINETIC METHODS . ... LABORATORY OF ELECTROCHEMICAL METHODS COLLOID AND INTERFACE CHEMISTRY DIVISION . ... LABORATORY OF EDUCATIONAL METHODS IN CHEMISTRY . ... LABORATORY OF NUCLEIC ACIDS AND NUCLEOTIDES CHEMISTRY OIL CHEMISTRY AND ORGANIC CATALYSIS DIVISION . ... LABORATORY OF PETROLEUM HYDROCARBONS CHEMISTRY ORGANIC CHEMISTRY DIVISION . ... Copyright (C) Chemisty Department of Moscow State University . ...

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• Moscow University Chemistry Bulletin Vol. 49, No. 1, P. 23 (2008)
• Moscow University Chemistry Bulletin Vol. 48, No. 3, P. 188 (2007)
• LABORATORY OF PHOTOCHEMISTRY

Schedule : Nonlinearity of Media and Structures, Nonlinear Testing . ... Guyer R. (invited) . ... Esipov I. B. Nonlinear Sound Wave Propagation in 2-D Hysteretic Medium . ... Berndt T. P. Simultaneous Probing of the Nonlinear Effect of a Plane Unbonded Interface on Incident Longitudinal and Shear Acoustic Waves as a Function of Amplitude and Pressure . ... R. E. (invited) . ... Korobov A. I. Influence of Internal Structure of Polycrystalline Copper on Its Nonlinear Elastic and Acoustic Properties . ...

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• Nonlinearity of Media and Structures, Nonlinear Testing