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software databases repairtoire repairtoire is an online database for systems biology of dna damage and repair. the database collects and organizes the following types of information: (i) dna damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in dna repair and (iv) diseases correlated with mutations in genes encoding dna repair proteins. the dna repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. in addition, a tool for drawing custom dna-protein complexes is available online. spliprot3d spliprot3d is an online database of representative experimentally determined and computationally predicted structures of proteins of the human spliceosome. modomics modomics is the first comprehesive database system for systems biology of rna modification. it integrates information about the chemical structure of modified nucleosides, their localization in rna sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions (including the available protein sequence and structure data). it also provides literature information, and links to other databases. the database can be queried by the type of nucleoside (e.g. a, g, c, u, i, m1a, nm5s2u etc.), type of rna, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.), and name or sequence of an enzyme of interest. options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of rna sequences and tabular forms with enzyme and literatiure data. the contents of modomics can be accessed through the world wide web at http://genesilico.pl/modomics/ rna bricks rna bricks is a database of rna 3d structure motifs and their contacts, both with themselves and with proteins. the database provides structure-quality score annotations and tools for the rna 3d structure search and comparison. rnarchitecture rnarchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding rnas, with a focus on structural similarities. the classification is hierarchical and similar to the system used in the scop and cath databases of protein structures. its central level is family, which builds on the rfam catalog, and gathers closely related rnas. consensus structures of families are described with a reduced secondary structure representation. evolutionarily related families are grouped into superfamilies. similar structures are further grouped into architectures. the highest level, class, organizes families into very broad structural categories, such as simple or complex structured rnas. some groups at different levels of the hierarchy are currently labeled as “unclassified”. for each family with an experimentally determined 3d structure(s), a representative one is provided. rnarchitecture also presents theoretical models of rna 3d structure and is open for submission of structural models by users. compared to other databases, rnarchitecture is unique in its focus on structure-based rna classification, and in providing a platform for storing rna 3d structure predictions. rnarchitecture can be accessed at http://iimcb.genesilico.pl/rnarchitecture/. *the classification is expected to evolve as new data become available and we would like to encourage all interested parties to submit their suggestions for improvement as well as 3d structure predictions* stand-alone protmap2d two-dimensional maps of contacts summarize interactions between amino acids in the structure. they reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. the overlap of the residue contact maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. moderna we developed a method for 3d homology modeling of rna structures. it requires a pairwise sequence alignment and a structural template to generate a 3d structural model of the target rna sequence via either a fully automated or script-based approaches. moderna is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library. rnamap2d rnamap2d is a software tool for calculation of contact and distance maps based on user-defined criteria, and to some extent, quantitative comparison of pairs or series of contact maps and visualization of the results. filtrest3d filtrest3d is a program for discrimination of a large number of alternative models of protein structure or protein-ligand structure against a set of restraints derived from low-resolution experimental analyses (such as cross-linking, mutagenesis, circular dichrosm etc.) as well as from computational predictions (e.g. solvent accessibility, amino acid contact maps). pyry3d pyry3d is a software tool for modeling of structures for large macromolecular complexes. it uses monte carlo simulation to sample conformational space and to identify the best fit of complex components structures into a density map. complex building process is based on distance restraints derived from experiments. statistical potentials rna-protein docking we developed two medium-resolution, knowledge-based potentials for scoring protein-rna models obtained by docking: the quasi-chemical potential (quasi-rnp) and the decoys as the reference state potential (dars-rnp). both potentials use a coarse-grained representation for both rna and protein molecules and are capable of dealing with rna structures with posttranscriptionally modified residues. in our tests that compared these methods to other published potentials, dars-rnp showed the highest ability to identify native-like structures. simrna simrna - a tool for simulations of rna conformational dynamics, including rna 3d structure prediction supernalign supernalign is a tool for flexible superposition of rna 3d structures. our program implements an iterative algorithm that splits rna structures into fragments and superimposes them using existing tools (currently r3d align). finally, the superimposed structures are saved to a .pdb file and a sequence alignment is generated. servers simrnaweb simrnaweb is a web server interface to the simrna method for rna 3d structure modeling method metaserver the genesilico metaserver is a gateway to a number of third-party methods for protein structure prediction (identification of domains, secondary structure prediction, fold-recognition, and finally, 3d model generation). users can submit a protein sequence (or alignment) by a single click, then analyze the summary of results generated by many methods, and finally predict the protein structure according to the "consensus" approach. frankenstein3d this tool builds protein models by recombining fragments of fold-recognition alignments. users can select a set of alignments from the output of the metaserver or provide their own alignments. the program will generate alternative models, identify fragments that either exhibit consensus conformation in different models or - in the absence of consensus - show the relatively best compatibility of amino acids with the environment of the rest of the model. these fragments will be recombined to create a hybrid model, which will be further optimized by trying alternative alignments in non-consensus regions to improve the sequence-structure compatibility. colorado3d this simple server facilitates visual presentation of three-dimensional (3d) protein structures. it is a gateway to a number of methods for evaluation of protein structure (anolea, prosaii, prove or verify3d), but also identifies buried residues

URL analysis for genesilico.pl

http://www.genesilico.pl/projects
http://www.genesilico.pl/software/stand-alone/statistical-potentials
http://www.genesilico.pl/people
http://www.genesilico.pl/resources
http://www.genesilico.pl/software/stand-alone/simrna
http://www.genesilico.pl/software/stand-alone/protmap2d
http://www.genesilico.pl/employment
http://www.genesilico.pl/software/stand-alone
http://www.genesilico.pl/software/databases
http://www.genesilico.pl/employment/other-positions
http://www.genesilico.pl/publications
http://www.genesilico.pl/achievements/awards
http://www.genesilico.pl/gallery
http://www.genesilico.pl/in-the-media
http://www.genesilico.pl/achievements/highlights

Whois Information

Whois is a protocol that is access to registering information. You can reach when the website was registered, when it will be expire, what is contact details of the site with the following informations. In a nutshell, it includes these informations;

DOMAIN NAME: genesilico.pl
registrant type: organization
nameservers: ns.genesilico.pl. [212.87.21.35]
ns1.net.icm.edu.pl.
created: 2002.04.23 13:00:00
last modified: 2017.04.11 15:14:28
renewal date: 2018.04.22 14:00:00

no option

dnssec: Unsigned


REGISTRAR:
home.pl S.A.
ul. Zbożowa 4
70-653 Szczecin
Polska/Poland
+48.914325555
+48.504502500
https://home.pl/kontakt

WHOIS database responses: http://www.dns.pl/english/opiskomunikatow_en.html

WHOIS displays data with a delay not exceeding 15 minutes in relation to the .pl Registry system
Registrant data available at http://dns.pl/cgi-bin/en_whois.pl

  REFERRER http://www.dns.pl/english/index.html

  REGISTRAR NASK

SERVERS

  SERVER pl.whois-servers.net

  ARGS genesilico.pl

  PORT 43

  TYPE domain

DOMAIN

  CREATED 2002-04-23

  CHANGED 2017-04-11

SPONSOR
home.pl S.A.
ul. Zbożowa 4
70-653 Szczecin
Polska/Poland
+48.914325555
+48.504502500
https://home.pl/kontakt
WHOIS database responses: http://www.dns.pl/english/opiskomunikatow_en.html

  NAME genesilico.pl

NSERVER

  NS.GENESILICO.PL 212.87.21.35

  NS1.NET.ICM.EDU.PL 213.135.57.10

  REGISTERED yes

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