... 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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• Screening by similarity

... 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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... 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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• Input Formats
• SDPsite

... 2 from allpy import dna . ... 6 def my_column_mark ( column , threshold ): . 7 """Helper to mark column (given as dict) by identity.""" . 8 count = {} . 9 for sequence , monomer in column : . ... 11 count [ code ] = count . ... 14 return "+" . ... 19 if column [ 0 ] is None or column [ 1 ] is None : . ... 25 def find_runs ( markup ): . ... 33 plus_positions = [] . ... 46 raise Exception ( "No blocks in alignment" ) . ... 66 for column in alignment . ... 68 markup = alignment . ...

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• allpy: 6e93a74d1917 test/usecase2.py
• allpy: 9665a6acdd53 test/usecase2.py
• allpy: 7a72febf12f6 test/usecase2.py

... The results will be also sent to you via E-MAIL to address: sherlock1991@rambler.ru . ... BRAJA MATITAAMVKDLRESTGAGMMDCKAALTENDGNMEAAQDWLRKKGLSKAA BURCA MAAITASMVAELRAKTDAPMMECKKALTEADGDLAKAEELLRVKLGNKAS RALPJ MAAITASMVAELRAKTDAPMMECKKALTEAEGNLEKAEEILRVKLGNKAG VIBCH -MAVTAALVKELRERTGAGMMECKKALVETNGDIELAIENMRKSGAAKAA VIBFM MATVTAALVKELRERTGAGMMECKKALVEANADIELAIENMRKSGAAKAA ECOLI MAEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAA PROMH MSGITAALVKELRERTGAGMMECKKALVEANGDIELAIDNMRKSGQAKAA ...

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• Global and Local Alignment of A.A Sequences
• petri_dish: 53672899af16 tk1.py

Электронная библиотека Попечительского совета . ... Moeller T.B. - Magnetic Resonance Imaging, Parameters and Positioning . ... Название: Magnetic Resonance Imaging, Parameters and Positioning . Автор: Moeller T.B. Аннотация: . Magnetic resonance imaging is a modality that is carried out under highly standardized conditions. ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Поиск книг, содержащих Control parameter :: Электронная библиотека
• Niedermeier R. - Invitation to Fixed Parameter Algorithms :: Электронная
• Smith R.C., Demetriou M.A. - Research Directions in Distributed Parameter

... 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

Evalign . Evalign is a computerised evaluation method for protein sequence alignment algorithm. It compares computer alignments with structural alignments of protein sequences and tells how correct your sequence alignment program is. It gives additional information on the characteristics of different alignment algorithms and shows types specific failings in alignment. ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Programming - Tools & Utilities - STL
• SAL- Mathematics - Statistics -- GLISREL
• SAL- Numerical Analysis - Optimization - GENBLIS

Nonuniqueness of shockwave structures in real gases: the Mach and/or regular reflection" . G.A. Tarnavsky . A number of nonuniqueness problems for the shockwave structures arising in high-speed flows at interaction of shocks with the Mach and/or regular reflection are considered. ... PostScript (in Russian) (645KB) . PDF (in Russian) (291KB) . PostScript. zip (in Russian) (230KB) . PDF. zip (in Russian) (180KB) . G.A. Tarnavsky e-mail: tarnav@itam.nsc.ru ...

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• "An algorithm of assigning the force parameters to atoms of organic molecules
• "Low-frequency approximation and the choice of optimal elastic parameters for
• "Influence of genetic algorithm parameters on the docking efficiency with the

... MPI_File_get_position . Returns the current position of the individual file pointer in etype units relative to the current view int MPI_File_get_position(MPI_File fh, MPI_Offset *offset) . ... All MPI routines in Fortran (except for MPI_WTIME and MPI_WTICK ) have an additional argument ierr at the end of the argument list. ierr is an integer and has the same meaning as the return value of the routine in C. In Fortran, MPI routines are subroutines, and are invoked with the call statement. ...

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• MPI_Pack | PARALLEL.RU - Информационно-аналитический центр по параллельным
• MPI_Unpack | PARALLEL.RU - Информационно-аналитический центр по параллельным
• MPI_File_get_byte_offset | PARALLEL.RU - Информационно-аналитический центр по

... The Influence of Microstructure of Media on Nonlinear Acoustic Parameter of Solutions . ... The acoustic nonlinear parameter B/A is strongly structure sensitive as it was shown in [Lesnyanskii et al. ... The values of parameters (Ye/Yid and derivative Ye with respect to pressure) are calculated from offered method [Balankina E.S. Proceeding of XI Session of the Russian Acoustic Society, Moscow, 2001 (http://www.akin.ru/RAO/sess11)] using volumetric-elastic properties of solutions. ...

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• Abstract (Invited)

... Online Services | ... Construct your query and output by sequental openings of needed fields. One output field must be selected (not be blank) at least. ... Query parameters: . Select for output . ... Energy (keV) . ... Y D H M S MS US NS PS FS AS EV KEV MEV or Stable . ... Energy of the ?-ray (keV) . ... Energy parameters of nucleus (B , Alpha energy, N, P separation energy) . ... Neutron separation energy (keV) . Proton separation energy (keV) . ... Excited energy(keV) . ...

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• CDFE => Online Services => Nucleus Ground State Parameters
• CDFE => Online services => Chart of nucleus shape and size parameters
• CDFE => Online Services => Calculator and Graph Engine for Atomic Nuclei

... Structure of Data . ... Catalog . ... Catalog: 206 clusters 32 clusters: known before 12 clusters: parameters from BVRI photometry @ SAO 1-m 0 clusters: parameters from UBVRI photometry @ Maidanak 1.5-m 26 clusters: parameters from 2MASS 168 clusters: new (2MASS) 142 clusters: parameters from 2MASS 26 clusters: embedded 0 clusters: parameters from BVRI photometry @ SAO 1-m 3 clusters: parameters from UBVI photometry @ ARIES 1.04-m 0 clusters: parameters from UBVRI photometry @ Maidanak 1.5-m . ...

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• SAI Open Star Clusters (SAI OCL) Catalog

... Received 15 April 2004 Accepted 21 April 2004 Online 30 April 2004 Dmitry V. Albov ,* Victor B. Rybakov, Eugene V. Babaev and Leonid A. Aslanov Department of Chemistry, Moscow State University, 119992 Moscow, Russian Federation Correspondence e-mail: albov @biocryst.phys.msu.su Comment In the course of our systematic study of the size effect of cycloalkane fragments on the reactivity of pyridine-based heterocycles ( Albov , Rybakov, Babaev ... 2004). ... Farrugia, L. J. (1997). ......

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• http://www.chem.msu.ru/eng/misc/babaev/papers/100e.pdf
• http://www.chem.msu.ru/eng/misc/babaev/papers/092e.pdf
• http://www.chem.msu.ru/eng/misc/babaev/papers/090e.pdf

... 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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• MRS structure functions
• C case
• General structure

... A new method is proposed that makes it possible to determine the parameters of the three-dimensional (3D) multiwell potential of off-center atoms from extended X-ray absorption fine-structure (EXAFS) data. ... The parameters of the multiwell potential for Ge atoms in the Sn 1-x Ge x Te solid solution as functions of temperature and composition (77<T<300 K, x>0.4) were obtained in the classical approximation. ...

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• New methods of measuring photoelectric parameters of silicon
• Local field and optical second harmonics generation in polar Langmuir-Blodgett
• EXAFS studies of semiconductors and ferroelectrics

... Among the methods of theoretical investigation of coordination compounds, molecular mechanics seems to be an optimal choice. However, conventional MM force fields typically do lack metal-related force field parameters. ... Let us calculate (MM) energy gradient for experimental structures using purely organic force field with no metal-dependent terms. ... In other words, thus calculated forces give an "imprint" for the derivation of metal-dependent forces. ...

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• Molecular Structure and Physicochemical Properties of Acetone-Chloroform...
• Molecular Structure and Conformations of Bicyclopentyl, C5H9-C5H9, as Studied
• Moscow University Chemistry Bulletin Vol. 53, No. 2, P. 81 (2012)

... Next: Plane tab Up: Client Previous: Connection to a Server Contents Index . Figure 2.4: Scan parameters. STM mode of operation. ... AFM mode of operation. ... All scan parameters can be configures in Parameters window (pic. ... Client part of `` FemtoScan '' software allows to control microscope operating in three different scanning modes - tunneling mode(STM), atomic-force mode (AFM) and resonance atomic-force (RAFM). ... It(Z) tab (STM mode), F(Z) tab (AFM mode), D(Z) tab (RAFM mode). ...

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• It(Z) tab (STM mode), F(Z) tab (AFM mode), D(Z) tab (RAFM mode).
• Surface scanning
• DSP board program

... About lab . ... Online Journal "Computer graphics and multimedia" (in russian) . ... Algorithms for calculating parameters of virtual scenes in computer vision tasks . ...

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... This form lets you to produce a list of hydrophobic clusters in a PDB file specified by user. Enter a 4-letter PDB code, e.g.: 1apl : . Search clusters: . ... between chains . Contacts between chains . Set #1 . ... Enter your e-mail here (optional): . ... List of atoms Strict Wide . Chains filter (1-20:A) . Show clusters not smaller than atoms . User data file in PDB format . ...

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• Inquiry information || Distances
• About authors ot this complex
• SDPpred