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

... annotate . ... structure, ignore_one_ss: fix a crash for alignments of >=3 sequences This bug is caused by multiple addition of ss markup in geometrical_cores(). ... 1 * new : add an argument not to save downloaded pdb ( CachedDownloadPdb ) . ... 3 * new : allow to load custom pdbs ( allpy . ... 4 * new : add pymol superimposition feature draft ( allpy . ... 7 * new : add `` parts ' ' argument to blocks3d() (allpy.structure) . ... 8 * new: add method blocks_from_homology() (allpy.structure) . ...

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• allpy: 9369dbad919d allpy/sequence.py
• allpy: 346a6cd4fc1d allpy/sequence.py
• allpy: d137df18a8bf test/usecase1.py

... 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

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 - GDE
• SAL- Other Scientific Fields - Chemistry, Biology Related - Protein Structure
• SAL- Other Scientific Fields - Chemistry, Biology Related - RnaViz

... 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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• Nhunt: program for nucleic acid sequence similarity search
• Align tool for DNA-protein complexes

... 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

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

Anchoring patterns and point mutations in pairwise alignments using AlignMe X-ray crystal structures have revealed that numerous membrane proteins, such as GPCRs or some secondary transporters, despite the lack of any detectable sequence similarity between them, still share very similar 3D structures. ... The novel feature allows the user to define any number of anchors with varying strength for improving the quality of pairwise alignments in challenging cases lacking notable sequence similarity. ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/120.pdf

. 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

... 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

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]

... 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
• [Comphep-common] Events to produce of LHAEF format

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

... 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

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)
• Лекция профессора Ю. Икухара

... 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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Enclosure structures of equal level line fields in the gradient filling problem" . Ivanov B.N. In this paper, the method of gradient filling of equal level line fields by color scale is considered. ... The root tree structure of equal level line enclosure is applied to the context analysis of all equal level line values in order to correctly specify the color values of their filling. A working algorithm of gradient filling of equal level lines is given. PostScript (in Russian) (2.67MB) . ...

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• "Routing on lattice-cellular structures"
• "TIM-parallelization in a shared memory model using OpenMP interface"
• Composition of infinitary structures