... add test for secondary structure markup for sequence Module protein_pdb was copied from blocks3d/protein_pdb.py. Sequence is created from string, pdb is loaded, ss-markup is applied. ... 8 by_name = {} . 9 """A dictionary of default markup name -> markup class.""" . ... 11 def update ( * args ): . ... values (): . ... 62 def to_record ( self ): . ... 91 for number , monomer in enumerate ( self . ... 131 def parse_value ( monomer , value ): . ... 139 def repr_value ( monomer , value ): . ...

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• allpy: 6134ae1dfdae allpy/markups.py
• allpy: 9b253b69f8f1 allpy/markups.py
• allpy: bf873e4054c2 allpy/markups.py

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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... 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 ::
• Levine J.P. - Algebraic Structure of Knot Modules :: Электронная библиотека
• Peters C.A., Steenbrink J.H. - Mixed Hodge Structures :: Электронная библиотека

... 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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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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... 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 protein sequence against PROSITE databank
• INTAS :: Global and Local Protein Matching
• Notes on searching by similarity

Probing -directed structured elements detection in RNA sequences S.V. Vinogradova Moscow State University, Faculty of Bioengineering and Bioinformatics , 119991, Moscow , GSP-1, Leninskiye Gory, MSU, 1-73 kintany@gmail.com R.A. Soldatov Moscow State University, Faculty of Bioengineering and Bioinformatics , 119991, Moscow , GSP-1, Leninskiye Gory, MSU, 1-73 solrust@mail.ru M.A. Mironov ... 2013) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/101.pdf

Scoring Matrices . Matrix Sequences Sequence Consisting of the first four Amino Acids in the Protein GYRB_ECOL: . ... Sequence Achieved by Substitution of the 2nd and 4th Amino Acid and Insertion between the 3d and 4th Amino Acid, in the Protein GYRB_ECOLI, to randomly chosen new amino acids: . ... Matrix Sequences Sequence Consisting of the First Nine Amino Acids of the Protein GYRB_ECOLI: . ... Sequence Consisting of 2nd, 3d, 7th, 8th and 9th Amino Acid Residues of the Protein GYRB_ECOLI: . ...

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• Summary Table Sequence
• Описание генома бактерии
• Conservative Amino Acid Residues

... 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
• C case
• MRS structure functions

... Composition of infinitary structures" . Ryabov G.G. and Serov V.A. The infinitary structure of an n -cube, global k -ary trees, and natural numbers are considered as a single genetic structure. A number of geometric characteristics of the shortest paths in an n -cube are specified and the properties of prime number symmetry among the natural numbers are studied on the basis of this structure. ... PDF (Full text in Russian, References in English) (382KB) . ...

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• "Enclosure structures of equal level line fields in the gradient filling
• "Routing on lattice-cellular structures"

... 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 - PF07978
• SDPsite - PF01398
• SDPsite - PF01399

... 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
• wLake program homepage
• Example of alignment

The first major global tomographic study was made by Professor Dziewonski in early 70's. The idea of this study was that the travel time anomalies observed for many ray paths, criss-crossing the Earth between various points near the Earth's surface and reaching different depths in its interior, could be resolved formally into a three-dimensional (3-D) model. ... How to use Harvard's 3-D Earth models? Now, you can download source codes in order to use Harvard's recent Earth models. ...

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• Global Seismic Tomography: A Snapshot of Convection in the Earth
• Bragg W. L. "The structure of silicates" - Все о Геологии (geo.web.ru)
• References

... 5DPK structure . Page of complex: 5DPK . Home Browse Download Help About Us . ... PDB ID . ... MUTY ADENINE GLYCOSYLASE BOUND TO A TRANSITION STATE ANALOG (1N) PAIRED WITH D(8-OXOG) IN DUPLEXED DNA TO 2.2 A . ... View in . ... Protein chains: . DNA chains: . ... 5dpk.pdb1.pdb . ... Pfam domains . ... Download file with secondary structure created by Stride . 5dpk.pdb1.pdb: [ download sequences in FASTA format ] . ... Click "SHOW" for view sequence . ... NPIDB team 2003 - 2016 . ...

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• NPIDB: Home

... MCAL_SATURDAY For recurrence : . ... mcal_event_set_category -- Sets the category of the streams global event structure . ... mcal_event_set_recur_none -- Sets the recurrence of the streams global event structure . mcal_event_set_recur_daily -- Sets the recurrence of the streams global event structure . mcal_event_set_recur_weekly -- Sets the recurrence of the streams global event structure . mcal_event_set_recur_monthly_mday -- Sets the recurrence of the streams global event structure . ...

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• mcal_event_init
• mcal_event_add_attribute
• mcal_event_set_recur_none

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

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 - Protein Structure
• SAL- Other Scientific Fields - Chemistry, Biology Related - RnaViz
• SAL- Numerical Analysis - Discrete Methods Related Tools - GrAL

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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... История кафедры . ... младших курсов . ... Уважаемые студенты 1-го, 2-го и 3-го курсов! ... Семинар кафедры проходит по пятницам в 15.20 в комн. ... а также на стендах кафедры на 2-м и 4-м этажах. Информацию о более ранних событиях см. в разделе "Жизнь кафедры" . ... 119991, Москва, Ленинские горы, д.1, стр.2, МГУ имени М.В.Ломоносова, физический факультет, кафедра фотоники и физики микроволн . ...

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Additional topic data, program-generated or from TWikiForms , is stored embedded in the topic text using META: tags . ... Meta Data Syntax . Meta Data Specifications . ... META:FORM . ... By default, TWiki stores topics in files on disk, in a really simple and obvious directory structure. ... Order of fields within the meta variables is not defined, except that if there is a field with key name , this appears first for easier searching (note the order of the variables themselves is defined). ...

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