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1. RNAalignment
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Ссылки http://bioinf.fbb.msu.ru/RNAAlign/RNAalignment.jsp?action=e -- 1.9 Кб -- 09.04.2016
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2. User's guide
... Run program . User's guide . Launching program . Input data format . ... Selecting the number of correlated pairs . ... In order to run thr program one needs Java 5.0 environment. ... At the end of computations one will be asked to review the selected number of correlated pairs. ... Note: One may redefine the number of correlated pairs by selecting the 'Edit' -> 'redefine correlated pairs number' menu item. Correlated pairs of positions are presented as a colored matrix, the heatmap. ...
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Ссылки http://bioinf.fbb.msu.ru/Prot-DNA-Korr/guide.html -- 6.5 Кб -- 11.01.2016
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3. RNA kinetics server
. Chain's growth rate . nt/sec . Nucleation constant . Final time . sec . Number of runs .
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Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/start.cgi -- 3.6 Кб -- 01.10.2012
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4. SDPlight
... SDPfox - the software package for the prediction of functional specificity groups and amino acid residues that determine the specificity using MPA. ... Amino acid residues that determine differences in protein functional specificity and account for correct recognition of interaction partners, are usually thought to correspond to those positions of a protein multiple alignment, where the distribution of amino acids is closely associated with grouping of proteins by specificity. ...
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Ссылки http://bioinf.fbb.msu.ru/SDPfoxWeb/algorithm.jsp -- 13.2 Кб -- 01.10.2012
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5. SDPlight
Using stand-alone SDPfox . ... To add a new specificity group, type in the group name and press "Add" . To change composition of specificity groups, select two groups: first, from which to remove sequences, and second, to which to add sequences. ... For a constructed grouping, it is possible to run SDPgroup, re-randomize grouping or move sequences according to the best weights (see algorithm) under the link 'SDPgroup'. ... These sequences are likely to be re-grouped after SDPgroup is performed. ...
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Ссылки http://bioinf.fbb.msu.ru/SDPfoxWeb/help.jsp -- 4.0 Кб -- 01.10.2012
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6. input
. Start word length . Max N missmatch . Min score . Gap parameter . Min information . Iterations . Max Loop . Min Energy .
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Ссылки http://bioinf.fbb.msu.ru/RNAAlign/input.jsp -- 3.7 Кб -- 01.10.2012
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7. SDPsite
... Algorithm & . ... 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). The analysis begins with a multiple alignment of a protein family. ... Predict SDPs only . Predict CPs only . Predict SDPs and CPs . Map a pre-identified list of SDPs and/or CPs onto a structure ...
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/index.jsp -- 3.0 Кб -- 01.10.2012
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8. SDPpred
... Many protein families contain homologous proteins that have a common biological function but different specificity. Given a multiple sequence alignment of a family divided into specificity groups, SDPpred predicts a set of alignment positions ( SDP, Specificity-Determining Positions ) that determine differences in the functional specificity. ... 2004) Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. ...
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Ссылки http://bioinf.fbb.msu.ru/SDPpred/index.jsp -- 5.3 Кб -- 01.10.2012
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9. SDPlight
... Help . ... Download SDPfox . SDPfox provides a novel phylogeny-independent method for prediction of specificity-determining positions (SDPs) and grouping sequences into functional sub-groups. You may use the form below to conduct a training set-driven analysis (i.e. predict protein specificity based on a set of known specificities) or download a JAR package that allows for ab initio specificity prediction. ... To get help, run java -jar SDPfox.jar. ...
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Ссылки http://bioinf.fbb.msu.ru/SDPfoxWeb/ -- 4.4 Кб -- 01.10.2012
[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/SDPfoxWeb/index.jsp -- 4.4 Кб -- 01.10.2012
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[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/SDPfoxWeb/index.jsp -- 4.4 Кб -- 01.10.2012
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10. Prot-DNA-Korr: main page
... Prot-DNA-Korr is a tool for studying sequence correlations between DNA-binding proteins and their binding sites. The program searches for such pairs of positions in alignments of proteins and their binding sites that demonstrate correlations between amino acid residues and bases. ... One only needs two alignments with the same number of elements: one of proteins and one of their respective binding sites. ...
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Ссылки http://bioinf.fbb.msu.ru/Prot-DNA-Korr/ -- 2.5 Кб -- 26.06.2012
[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/Prot-DNA-Korr/main.html -- 2.5 Кб -- 26.06.2012
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[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/Prot-DNA-Korr/main.html -- 2.5 Кб -- 26.06.2012
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11. Bioinformatics Group of FBB MSU
... Andrey A. Mironov [page] . Aleksandra B. Rakhmaninova [page] . Mikhail S. Gelfand [page] . Dmitri D. Pervouchine [page] . ... Lena Stavrovskaya [page] . PhD Students . Dmitriy Vinogradov [page] . ... Yura Korostelev [page] . Katya Khrameeva [page] . ... Undergrad Students . ... SDPpred (Specificity-Determining Positions Prediction) Server [version 0.1] . ... RNA kinetics . Server for multiple alignment of RNA sequences . ... Subscribe to Mironov group meeting . ...
12. Algorithm
... The program calculates the correlation between each pair of columns [ i, j ]: one from the proteins alignment, and the other from the site alignment. As a measure of correlation, the mutual information is used: . ... Arrays of 20 aminoacids and 4 nucleotides respectively. Observed frequency of aminoacid x being in position i and nucleotide y being in position j . ... Calculated as frequency of aminoacid x in column i multiplied by frequency of nucleotide y in column j . ...
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Ссылки http://bioinf.fbb.msu.ru/Prot-DNA-Korr/algorithm.html -- 3.7 Кб -- 17.12.2010
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13. RNA kinetics server
... 7.6 . ...
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Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/example.html -- 30.0 Кб -- 12.10.2010
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14. RNA Kinetics main page
... The software models the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule. The result of the modeling is a kinetic ensemble, i.e. a collection of RNA structures that are endowed with probabilities, which depend on time. ... 19, Moscow, 127994, Russia. ... Danilova, L.V., Pervouchine, D.D., Favorov, A.V., Mironov, A.A. (2006) RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA. ...
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Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/ -- 4.2 Кб -- 12.10.2010
[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/index.html -- 4.2 Кб -- 12.10.2010
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[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/index.html -- 4.2 Кб -- 12.10.2010
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15. RNA Kinetics: Theory
In our model for RNA secondary structure formation we assume that each of the candidate helices (see definition in the main text) may exist in two states. A helix can be completely zipped, or it can be completely decayed. ... The following schema is used to estimate the effective transition constants between zipped and decayed states: . ... To determine the kinetic constants, we use the transition state theory, which is often used in chemical kinetics (Figure 2). ... Transition . ...
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Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/theory.html -- 14.9 Кб -- 12.10.2010
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16. RNA Kinetics: Result explanation
List of candidate helices . For each helix: plot of its probability vs. time . List of structures . For each structure: plot of its probability vs. time . ... Helix ID (a number used to identify the helix in structures) . ... Kinetic constant for helix decay . Plot of helix's probability vs. time . Helix probabilities . Summary plot of helix probabilities vs. time . ... Plot of structure's probability vs. time . ... Summary plot of structure's probabilities vs. time . ...
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Ссылки http://bioinf.fbb.msu.ru/RNA/kinetics/explanation.html -- 4.5 Кб -- 12.10.2010
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17. SDPsite - Gallery of examples
... Algorithm & . Format requirements . Contact us . Gallery of examples . SDPsite was applied to 124 families fron the Pfam database . ...
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/gallery.html -- 10.0 Кб -- 06.06.2008
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18. SDPsite - PF01883
... This family contains a protein with resolved 3D structure: Q9WYV7_THEMA/8-83 , pdb ID: 1uwd . SDPsite predicts following important positions (numbering corresponds to 1uwd ): . ... 32L, 24G, 48M, 10D, 34Y, 18V, 25L, 57L, 50M, 13N, 26D, 31G, 17N, 72I, 68A, 27V, 33V . ... 55C, 20D, 21F, 51T, 22E, 31G, 80V, 18V, 56P, 33V, 30L . ... 18V, 20D, 21F, 22E, 24G, 25L, 26D, 27V, 30L, 31G, 32L, 33V, 48M, 50M, 51T, 55C, 56P, 57L . ... 10D, 13N, 17N, 68A, 72I . ... Associated grouping: . Group 1 . ...
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/examples/PF01883.html -- 4.4 Кб -- 06.06.2008
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19. SDPsite - PF01903
. Home & Submit job . Algorithm & . Format requirements . Contact us . Gallery of examples . This family contains a protein with resolved 3D structure: CBIX_ARCFU/10-119 , pdb ID: 1tjn . SDPsite predicts following important positions (numbering corresponds to 1tjn ): . SDPs: . CPs: . Best cluster: . Second best cluster: . Mapping predictions onto structure of 1tjn : . Associated grouping:
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/examples/PF01903.html -- 3.4 Кб -- 06.06.2008
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20. SDPsite - PF02362
... SDPsite predicts following important positions (numbering corresponds to 1yel ): . ... Associated grouping: . Group 1 . ... Q9SHV3_ARATH/13-105 . ... O81782_ARATH/13-105 . ... O81781_ARATH/13-105 . ... Q9SB79_ARATH/13-105 . O65098_BRAOB/9-94 . Q84J39_ARATH/9-94 . ... Q9SB80_ARATH/13-105 . Q84WP3_ARATH/14-107 . Q9SJ97_ARATH/746-841 . Q9SJA0_ARATH/9-98 . ... O81778_ARATH/13-105 . ...
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/examples/PF02362.html -- 8.9 Кб -- 06.06.2008
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