... annotate . ... 3 This release collects a lot of changes that happened during half year . ... 8 * greatly improved markups support and markups IO . ... 12 * and a lot of work on ` blocks3d ` and ` pair_cores ` with many new features , . ... 39 * new : added ` MarkupIOMixin ` which simplifies defining savable markup classes . ... 40 * new : added pre - defined generic markups for simple data types ( int , char , . ... 69 * new : File format 'markup' for storing alignment with arbitrary markups . ...

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• allpy: 2b3cad50c2b1 NEWS

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

... 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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• PLANdbAffy: probe-level annotation database for Affymetrix expression
• 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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• Databases
• Genebee Predicted Annotation - Advanced
• Bioinformatics portal, Moscow State University

... Query: E. coli K12 tRNA (valV, selC, asnV, leuT, argZ from EMBL entry U00096 ) . ... BLASTN (both) | ... Nhunt . ... BLASTN (optimal): 3.5 s . BLASTN (default): 0.8 s . ... Nhunt: 7 s The program Nhunt surpass all other tested programs in sensitivity. ... Nhunt BLASTN (optimal): 2.9 s . ... Nhunt: 3.7 s BLASTN with default parameters actually cannot find any significant homologues. ... Nhunt-3: 1.7 s BLASTN with default parameters actually cann't find any significant homologues. ...

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

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

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/2013/abstracts/abstracts/18.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/4.pdf

... 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

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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. 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