log . ... Thu, 05 Apr 2012 19:27:32 +0400 . ... Automated merge with ssh://kodomo/allpy . ... Tue, 03 Apr 2012 12:31:05 +0400 . Boris Nagaev . ... Merge fix of typo in algorithm name Bron?Kerbosch from default into 1.4.2 1.4.2 . ... Mon, 26 Mar 2012 22:09:09 +0400 . Boris Burkov . ... Sun, 25 Mar 2012 22:54:35 +0400 . ... Fri, 23 Mar 2012 16:52:31 +0400 . ... Tue, 20 Mar 2012 22:08:55 +0400 . ... pair-cores: add a patch upgrading allpy.structure 1.4.2 . ... Thu, 15 Mar 2012 23:17:23 +0400 . ...

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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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• SDPpred
• S publications

. A program for alignment of structures of DNA-protein complexes . Home . Feedback . Help . About . Input PDB code of the first complex: and chain of the protein (optional): . Input PDB code of the second complex: and chain of the protein (optional): . If you get stuck with program input, try example data and click Align! Example data . 2016

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• ConClus
• StructAlign help

... 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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• AliGraf - GeneBee Graphical Alignment Help
• Screening of pattern or alignment against PROTEIN databank
• AliComp - GeneBee Alignment Comparison Help

... wLake 1.7 . wLake is a tool which allows to identify clusters of a structural water molecules in given superimposed 3D structures. Put your coordinates in PDB format into the text area. Select a distance threshold. Two water molecules from different structures will be concidered as located in the same space point if the distance between centers of oxygen atoms is less than this threshold. ... EACH STRUCTURE INCLUDING ITS WATER MOLECULES MUST BE PRESENTED AS SEPARATE MODEL: EXAMPLE. ...

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• Blocks finder
• Geometrical core
• SVETKA, a program for multiple sequence alignments analysis

Электронная библиотека Попечительского совета . ... Greibach S.A. - Theory of Program Structures: Schemes, Semantics, Verification . ... Название: Theory of Program Structures: Schemes, Semantics, Verification . Автор: Greibach S.A. Аннотация: . ... Array, program scheme augmented by arrays 7-52 . ... Loop program 4-49 . ... Program scheme, always halting program scheme 3-13 . Program scheme, free program scheme 3-18 . ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Michalewicz Z. - Genetic algorithms + data structures = evolution programs ::
• Royer J.S. - A Connotational Theory of Program Structure :: Электронная
• Mulkers A. - Live Data Structures in Logic Programs: Derivation by Means of

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- Computer Graphics, Images Signals - Miscellaneous Software
• SAL- Numerical Analysis - Discrete Methods Related Tools
• authcert - DES validation program

... 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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• Algorithm
• Site Cluster

... Markup We sometimes (very often) want to add marks on an alignment. ... Our definitions Examples What works Projects using allpy Future Converting alignment format alignment = protein. Alignment ().append_file( input_file, format= genbank ) alignment .to_file(output_file, format= fasta ) Converting alignment format -- the uncensored version from allpy import protein input_file = open( input_file.fasta ) output_file = open( output_file.fasta , w ) alignment = protein ...

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• Structure Alignment

All these programs are written on FORTRAN 77. ... Listing of the main routine, the function and the results ( fig4_2.txt ). Listing of the subroutines ( listing_01.txt , listing_01.zip ). ... The block (the main routine, the function and the subroutines (+general)). ( application_01.zip ). ... General programs. ... All listings of the subroutines ( all_listings.zip , all_listings.txt ) and the main routines with the functions and the results ( all_figures.zip , all_figures.txt ). ...

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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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• Program of course
• The layout of a program
• Dynamic HTML in Communicator

. A system for analysis of information structure of programs. Stefanov C.S. An autonomous system for analysis of information structure of programs is described. The system is intended for adaptation of sequential programs for running on parallel computing systems. PostScript (in Russian) (72.1MB) . PDF (in Russian) (1.16MB) . PostScript. zip (in Russian) (2.66MB) . PDF. zip (in Russian) (1.02MB) . Stefanov C.S. e-mail: cstef@parallel.ru

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• "The package of application programs for the robust multigrid technique:
• "Heuristic algorithms of mapping MPI-programs onto multicluster computer and
• "The MEL program for the atomistic modeling of functional layers in solar...

UGENE toolkit: Bioinformatics "Swiss army knife" Yuriy Vaskin Novosibirsk State University, Novosibirsk, Pirogova St. 2, 630090, vaskin90@gmail.com M. Fursov NCIT Unipro, Novosibirsk, Lavrentieva ave. 6/1, 630090, mfursov@unipro.ru In the age of information technologies it is not surprising that biologists use special computer programs in their day-to-day work. ... Currently there are a lot of data formats and types which are spread throug various biological databases. ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• Program of MCCMB'05
• MCCMB'11 posters

LIDER INVESTIGATOR - A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences; . ... Zoological Institute of Russian Academy of Sciences; . ... Object of study must be different types of the ecosystems; being subjected influences of invasion species (sea, freshwater, agro-ecosystems and etc); . Evaluation of ecological and economic damage from invasion species in Russia; . ... Preparing the forecasts (supposed migrant list and evaluation of consequences); . ...

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• Scientific programs and projects
• Structure and Staff

The M.V. Lomonosov Moscow State University is organizing a traditional International Conference "BIOCATALYSIS-2007" in 17-22 June 2007 (preliminary dates were changed). ... Structure, catalytic mechanism and protein engineering of enzymes. ... EURO . ... In view of a limited number of ship cabin passengers, the Organizing Committee is asking to apply for participation at BIOCATALYSIS-2007 Conference, to send the Abstracts and to pay the Registration Fee not later than the deadlines indicated above. ...

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... 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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• DSP board program
• FemtoScan Online program
• Evgeny Menshikov

... The main problem is increasing the recognition rate of some recognition engines, working in some restricted domains, such as telephone time-table question-answer systems and so on. ... Our algorithms allow user to get recognition variants, which are right sentences in some formal language. ... We suppose that BRE can produce a set of recognition variants in the form of the "complex chain". ... Length of complex chain is the number of vertexes in its graph. ... const*n^2 . ...

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DVM-system of parallel program development . Goals and structure . ... 2.1 C-DVM and Fortran DVM parallel program development . ... Using C-DVM and Fortran-DVM languages a programmer deals with the only version of the program both for sequential and parallel execution. ... These rules are syntactically organized in such a manner that they are "transparent" for standard C and Fortran compilers and doesn't prevent DVM-program execution and debugging on workstations as usual sequential program. ...

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• Fortran DVM compiler. Detailed design
• DVM debugger. Detailed design. Part 4
• Fortran DVM language description

... Academic . ... Academic Departments . ... Partners . Conferences . ... All partners . ... The international academic conference . ETHNIC PRESS GENESIS, STRUCTURE, DEVELOPMENT TRENDS . ... Conference proceedings will be published at the endљ . of the Conference as a collection of scientific articles and available in electronicљ . ... Organizing Committee address: Department of Journalism, Room 325 A, 3d floor, Main Academic Building, 42 Kulakovskogo St., Yakutsk, 677000. ...

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• Full-time programs :: Department of Journalism, M. V. Lomonosov Moscow State

We provide the user with a possibility to attach his own codes to the n_comphep_f(c) and genEvents programs. ... CompHEP archive file num_f(c).a contains some patch programs. ... In the case of n_comphep_f(c) command the following instruction does this job: . ... It is assumed that the above command is started from within the user's directory results which contains sources or their archives. The genEvents file is disposed in the $COMPHEP directory and generally cannot be modified by the user. ...

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• History and personal contributions
• C case
• Fortran case