... file . ... 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. ... 3 * new : Alignments , Sequences and Blocks now can have Markups , see the wiki . ... 5 * new : processor allpy . ... 6 * new : method allpy . ...

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• allpy: allpy/dna.py annotate
• allpy: allpy/rna.py annotate
• allpy: 835efa2a8c71 .hgignore

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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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/2015/proceedings/abstracts/179.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• Program of MCCMB'05

... 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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• Notes on searching by similarity
• Genebee Predicted Annotation - Advanced
• Bioinformatics portal, Moscow State University

... 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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• Niederreiter H. - Random number generation and quasi-Monte Carlo methods ::
• Heggins D., Taylor W. - Bioinformatics: Sequence, Structure and Databanks ::
• Behrens J. - Adaptive Atmospheric Modeling: Key Techniques in Grid Generation,

... 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
• PLANdbAffy: probe-level annotation database for Affymetrix expression
• Example of 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
• Site Cluster

Protein Structure Software . Dr. Andrew C.R. Martin has written various programs and libraries for both general applicability and for use with protein structure. Here are the listings for programs: . ... ProFit -- Designed to be the ultimate(?) protein least squares fitting program. ... The author also developed an extensive library of C routines for the manipulation of protein structures. ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - RnaViz
• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE
• SAL- Programming - Languages Compilers - Rigal

... PDF (Full text in Russian, References in English) (1.47MB) . PDF. zip (Full text in Russian, References in English) (1.30MB) . Plenkin A.V. тАУ Nuclear Safety Institute, Russian Academy of Sciences; ulitsa BolтАЩshaya TulтАЩskaya 52, Moscow, 115191, Russia; Ph.D., Scientist, e-mail: golden_dragon_84@mail.ru . Chernyshenko A.Yu. тАУ Institute of Numerical Mathematics, Russian Academy of Sciences; ulitsa Gubkina 8, Moscow, 119333, Russia; Ph.D., Scientist, e-mail: chernyshenko.a@gmail.com . ...

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• "A detection method for mass-generated unnatural texts based on the topical
• "Generation of cycles of map cells for a simple planar graph"
• "A program environment for mesh generation, refinement, and partition and for

... 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
• Nhunt: program for nucleic acid sequence similarity search
• StructAlign help

... Bond lengths : 0.936 . ... 2 модель Structure Z-scores, positive is better than average: 1st generation packing quality : -3.134 2nd generation packing quality : -2.433 Ramachandran plot appearance : -0.028 chi-1/chi-2 rotamer normality : -2.052 Backbone conformation : -0.571 RMS Z-scores, should be close to 1.0: Bond lengths : 0.927 Bond angles : 1.301 Omega angle restraints : 0.809 Side chain planarity : 0.478 (tight) Improper dihedral distribution : 1.025 Inside/Outside distribution : 1.083 . ...

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• Conservative Amino Acid Residues
• Второй семестр
• Structure Alignment

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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Fortran-DVM Compiler . Detailed design . ... 3.1 Parsing . 3.2 Transforming parse tree . 3.3 Generating code in Fortran 77 . ... 4.2 Symbol and Type table . ... This report presents the detailed description of the Fortran-DVM (FDVM) compiler implementation. ... The input to the compiler is source code in Fortran DVM or HPF-DVM language. ... It is designed as an open C++ class library that provides a set of parsers, a structured parse tree, a symbol and type tables for a user. ... dvm.cpp . ...

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... Langmuir-Blodgett (LB) technique becomes now an effective tool producing thin molecular films of desired composition and structure. Its development gave rise to numerous experimental investigations of LB films as nonlinear optical wave guides devices. ... It seems to show that effects of LB films structure on their nonlinear optical parameters are mainly connected with specifics of their local field distribution. ...

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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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Additional topic data, program-generated or from TWikiForms , is stored embedded in the topic text using META: tags . ... Meta Data Syntax . Meta Data Specifications . ... META:FORM . ... By default, TWiki stores topics in files on disk, in a really simple and obvious directory structure. ... Order of fields within the meta variables is not defined, except that if there is a field with key name , this appears first for easier searching (note the order of the variables themselves is defined). ...

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. annotation of talk . Dr. V.N. Lukash (Astro Space Centre of Lebedev Physics Institute) . Dark energy's action on formation of the large scale structure in the Universe . The focus of this talk is on the dark energy problem. We show that generation of the large scale structure in the Universe proceeds in the period from 1 to 20 Gyrs. Dark energy affects the structure formation dramatically and can be measured "weighting" the structure in time.

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Annotation of diploma "Fiber-based visualization of biomarkers by Raman scattering and optical harmonic generation" The use of multicore fiber-optic probes for different methods of high spatial and temporal resolution visualization is shown. multicore fiber-optic setup was developed and applied for delivering the pump radiation and Raman signal, that allowed us to visualize the spatial distribution of Raman active resonances of matter. ...

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• Publication
• Публикация

... 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
• Getting started with LanHEP
• Main facilities

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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