... annotate . ... Fixed a serious bug with saving sequence markups when alignment does not have all of the sequence monomers . ... dendik@1076 . ... 3 This release collects a lot of changes that happened during half year . ... 12 * and a lot of work on ` blocks3d ` and ` pair_cores ` with many new features , . ... markup ` ( not to be . ... 68 * new : Alignments , Sequences and Blocks now can have Markups , see the wiki . ... 69 * new : File format 'markup' for storing alignment with arbitrary markups ...

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• allpy: 2b3cad50c2b1 NEWS
• allpy: 94ba384cfa50 NEWS
• allpy: afed1fd8920c NEWS

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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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
• Molecular biology databases
• ETS sequence conservation

... 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
• 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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• Bioinformatics portal, Moscow State University
• Databases
• Screening of pattern or alignment against PROTEIN databank

. Nhunt: program for nucleic acid sequence similarity search . Download . User manual . Application examples . License . News . About . Authors publications . Contacts . Web interface . Copyright 2010-2011 Yury Pekov

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

... 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

Bioinf ormatic analysis of diverse protein superf amilies to design improved enzymes Dmitry Suplatov , Nikolay Panin, Tatyana Shcherbakova, Ilyas Khaliullin, Vytas Svedas Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and F aculty of Bioengineering and Bioinformatics ... D. Suplatov, E. Kirilin, V. Takhaveev, V. Svedas (2014) Zebra: web-server for bioinformatic analysis of diverse protein families, J.Biomol.Struct.Dyn., ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/4.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf

Next: SYSTEM CALL: msgget() Up: Internal and User Data Previous: Kernel msqid_ds structure . The kernel stores permission information for IPC objects in a structure of type ipc_perm . ... struct ipc_perm { key_t key; ushort uid; /* owner euid and egid */ ushort gid; ushort cuid; /* creator euid and egid */ ushort cgid; ushort mode; /* access modes see mode flags below */ ushort seq; /* slot usage sequence number */ }; . ... Finally, the slot usage sequence number is stored at the end. ...

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• Internal and User Data Structures
• Internal Data Structures
• Kernel semid_ds structure

. 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
• Global and Local Alignment of A.A Sequences

... They in fact form surfaces that can be treated as interfaces between polar aqueous solutions and non-polar environment of phospholipidic side chains. ... That's why our idea was to study the behaviour of amino acid residues, as monomer units of proteins, in an interfacial system. Objective By means of molecular dynamics simulations we intended to study the properties of amino acid residues in a system containing liquid-liquid interface between water and hexane, which we took as a non-polar phase. ...

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

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
• Abstract

... 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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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
• A generic DII interface

... Research programm of the laboratory-chair< . ... Laboratory-chair of Discrete mechanics on a microscopic scale . ... Thus the structures of the physical world are not physical objects but physical processes. ... The primitive entity is called a material point. ... The value of the property “existence” of the material point varies from “the material point does not exist” to “the material point exists” by this process. ... Let call this structure a dynamical graph or a d-graph. ...

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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]
• download:rn-080423 [CompHEP]

... 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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• [Comphep-common] Events to produce of LHAEF format
• General structure
• Graphical interface

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)
• Спецкурсы кафедры "Химическая энзимология. Основы биоинформатики и
• Moscow University Chemistry Bulletin Vol. 48, No. 3, P. 188 (2007)