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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• Molecular biology databases

... 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

... 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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• Site Cluster
• SDPsite

The files containing information about Affymetrix microarrays were downloaded from the official Affymetrix site. ... Probe sequences were mapped to the genome using Blat. ... The hits found "probe alignment regions" were . ... We annotated each probe alignment region using the mRNA and EST alignments provided by UCSC, considering only . ... The textual part of the interface consists of probe information section, probe alignment section and transcription state . ... Each gene and each probe alignment . ...

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• wLake program homepage
• Geometrical core

Home . Database of structures of nucleic acid - protein complexes . ... List of complexes . Pfam families . SCOP families . Interaction classes . ... NPIDB . ... Information on SCOP and Pfam domains detected in protein chains is presented. ... Each family has its own web page with the list of entries that include domains of the family. ... List of SCOP domains occurred in DNA-protein and RNA-protein complexes is organized in tree-like form, according to the SCOP classification. ...

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... annotate . ... optimization of rasmol_homology: keep structure loaded of two sequences only One of steps of this program is superimposition of all sequences with main sequence and saving of all structures to pdb file. ... To implement this optimization methods supeimpose and save_pdb of alignment were replaced with methods with same names of sequence. ... dendik@534 . ... 2 ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb/data/monomers/components.cif.gz . ... 3 codes_py = allpy/data/codes.py . ... 11 doc:...

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• allpy: NEWS annotate
• allpy: a17d913cccef allpy/markups.py
• allpy: allpy/rna.py annotate

BLASTCLUST - BLAST score-based single-linkage clustering. ... BLASTCLUST automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in case of proteins or Mega BLAST algorithm for DNA. ... The primary input format for BLASTCLUST is a FASTA-format sequence file. ... Another type of input is a sequence hit-list previously saved by BLASTCLUST (in this case BLASTCLUST will use pre-computed HSP data instead of making de novo comparisons). ...

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• Summary Table Sequence
• page of Dovgan Kirill

This page is intended for presentation of astronomical databases maintained at Sternberg Astronomical Institute, Moscow University. These Projects are partially sponsored by INTAS and RFBR foundations. Hypercat mirror , (RFBR #99-07-90067) . ... Catalogue of Spatially Resolved Kinematics of Galaxies , (RFBR #99-07-90067) . ... Online access to SAI catalog of SN Light Curves . ... We have implemented Web gateways to some of our catalogs. ... HTTP access to SAI Catalog of Supernovae Stars . ...

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• Отдел Изучения Галактики и переменных звезд
• SAL -- Scientific Applications on Linux -- New Items Added in 2000/11 and
• Sternberg Astronomical Institute

... 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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• Notes on searching by similarity
• BLAST Basic Overview
• Bioinformatics portal, Moscow State University

Alexey Rastorguev's links to DataBases and Catalogs: . ... Open Clusters and Galactic Structure База данных и каталог рассеянных скоплений Галактики . ... USNO: Astronomical Applications Каталоги и базы данных - проекты Морской Обсерватории США . ... HST Science Data Archive Архив данных HST . CFHT Data Archive Архив данных CFHT . ... USNO Recommended Star Catalogs (Zacharias N. et al.) ... USNO Star Catalogs Каталоги USNO . ... USNO-B1.0 Catalog Астрометрический каталог USNO-B1.0 . ...

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• Data bases of Natural Satellites. Documentation. Structure

Data structuring and formalization in the hybrid database on molecular spectral constants (ISMOL)" . Kochikov I.V., Kuramshina G.M., Samkov L.M., Sharapov L.A., Sharapova S.A. This paper presents the principles of data representation and structuring in the information system ISMOL - a hybrid database on molecular constants of organic compounds existing in raw oil and its refinement products. ... Kochikov I.V. e-mail: kochikov@tm-net.ru . Kuramshina G.M. e-mail: kuramshi@phys.chem.msu.ru . ...

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• "Integration of Fuzzy c-Means Clustering algorithm with PostgreSQL database
• The "Areola" system database

Электронная библиотека Попечительского совета . ... Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the Internet . ... Название: Bioinformatics: A Biologist's Guide to Biocomputing and the Internet . Автор: Brown S.M. Аннотация: . A practical overview of bioinformatics, for researchers. ... Also discusses and evaluated programs for PCs, the Internet, and mainframes. DLC: Bioinformatics. ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Attwood T.K., Parry-Smith D.J. - Introduction to bioinformatics :: Электронная
• Raychaudhury S. - Computational text analysis for functional genomics and
• Heggins D., Taylor W. - Bioinformatics: Sequence, Structure and Databanks ::

... 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 => Useful links

Roman Sutormin rsutormin@gmail.com Professional experience 05/2013 ­ present: Lawrence Berkeley National Laboratory (Berkeley, CA, USA) Software developer Development of JSON based storage system used for keeping biological data involved in public KBase services. ... 10/2009 ­ 08/2011: Mail.Ru Group (Moscow, Russia), Software developer Support and development of data warehouse (PostgreSQL) and administration web tool (JBoss + GWT) on serverside of MMO game "Allods Online". ... 2013 Jul 1514(1):476. ...

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• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2013.pdf
• http://storage.bioinf.fbb.msu.ru/~roman/mol_biol_mosk_2006.pdf

Evolution and Classification of GH101 Family Glycoside Hydrolases: Four Years Later Daniil G. Naumoff S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/2, Moscow 117312, Russia; daniil_naumoff@yahoo.com Recent progress in geno me sequencing resulted in a rapid growth of the sequence databases. The number of known representatives of all protein families has increased dramat ically. ... This family was described in 2005 [2]. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/35.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf

... Structure of Data . ... Catalog . ... In SAI OCL Catalog, we introduce our work on investigation of the Milky Way system of open star clusters. The main goal of our study is a search for new clusters using huge surveys. 168 new clusters have been already discovered by us using J,H,Ks data from 2MASS point source catalog. ... For 141 new clusters, we found their physical parameters using J,H,Ks data from 2MASS catalog and, for a number of clusters, our UBVRI CCD observational magnitudes. ...

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• SAI OCL Catalog The Team
• SAI OCL Catalog Structure
• SAI OCL Catalog Publications

. From Homo sapiens (human) Search Entrez gene_id UniGene Keyword Gene GeneBank edas id for Entrez gene_id is Entrez gene database identifier (e.g. 12345 ) . UniGene is UniGene cluster identifier (e.g. 1234 ) . Keyword is word or phrase in the UniGene cluster title (e.g. breast cancer ) Gene is gene name (e.g. BRCA1) . GenBank is GenBank accession (e.g. M94203 ) . edas_id is EDAS identifier (e.g. 123 ) .

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• EDAS2 - Alternative Splicing DataBase.

XAFS spectroscopy is widely used in physics, materials science, chemistry (especially in catalysis and coordination chemistry), biology, geochemistry and environmental science. ... This is an interface to the Glimpse -based search engine which enables you to find published papers in different fields of x-ray absorption spectroscopy -- XAFS, EXAFS, XANES, NEXAFS, SEXAFS, XEOL, and EXAFS-like phenomena in photoemission, electron-energy-loss spectra and so on. ... Database Search Form . ...

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... Chemistry of Coordination Compounds . ... Inorganic Synthesis . ... CLUSTERS AND EXTENDED METAL-METAL BOND SYSTEMS IN INORGANIC COMPOUNDS . ... Cluster compounds, structure & bonding, quantum chemistry . ... Inorganic synthesis, bismuth clusters, metal subhalides . ... inorganic synthesis, clusters, mixed chalcogenides . ... Design, synthesis and investigations of inorganic compounds featuring extended systems of homo- and heterometallic bonds of varying (1D, 2D) dimensionality. ... Kuznetsov . ...

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• Inorganic Synthesis Laboratory - Supramolecular and Cluster Compounds
• Synthesis, Crystal and Electronic Structure of Subvalent Metal Compounds

... Computer software has been developed for crystal chemistry analysis of arrangement of molecules in organic crystals on the basis of concepts worked out in the studies conducted by P.M.Zorky et al. ... The standard crystal chemistry analysis includes: . ... Constructing various graphic representations of the crystal structure and of its fragments, which clearly demonstrate arrangement of molecules, in particular, constructing representations of the most close molecule-molecule contacts. ...

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• Slovokhotov, Yuri Leonidovich
• Moscow University Chemistry Bulletin Vol. 51, No. 5, P. 339 (2010)
• Molecular modelling isomorphous substitutions W on Rh in crystal lattice like