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CDART / Conserved Domain Architecture Retrieval Tool
Uses the domain definitions and annotations from the Conserved Domain Database (CDD) (which imports alignments from SMART and Pfam) and RPS-BLAST to allow users to rapidly query the Entrez Protein database by domain. To use this tool, a user enters a protein of interest, and RPS-BLAST is run on the protein to deduce its domain architecture. This domain architecture is then used to query CDART's database to find proteins with similar domain architectures, and the resulting proteins are displayed in a compact list.
Batch cd-search / Batch conserved domain search
A web-based tool for the detection of structural and functional domains in protein sequences. CD-Search combines the sensitivity of carefully constructed search models based on multiple sequence alignments with the speed and significance statistics of the BLAST1 software. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family.
CCR XP / Clusters of Conserved Residues XP
Explores clusters of conserved residues. CCR XP is a web application that automates the detection and analysis of such clusters in protein structures. It is composed of two input modules: (i) CCR XP lite that extracts file from atom records, finds aligned sequences, calculates conservation scores, clusters conserved residues and reports structural properties of each residue, and (ii) CCRXP ADV, an advanced version that allows users to select a number of filtering and clustering options that can be used.
AL2CO
Performs conservation analysis in a comprehensive and systematic way. AL2CO calculates a conservation index at each position in a multiple sequence alignment using several methods. The algorithm of AL2CO program performs calculations in two steps. First, amino acid frequencies at each position are estimated. The conservation index is then calculated from these frequencies. An optional third step allows the user to average the conservation indices over a window covering a selected number of positions.
PatchFinder
A methodology that automatically identifies patches of conserved residues that are located in close proximity to each other on the protein surface. PatchFinder is based on the following steps: (1) Assignment of conservation scores to each amino acid position on the protein surface. (2) Assignment of a score to each putative patch, based on its likelihood to be functionally important. The patch of maximum likelihood is considered to be the main functionally important region, and the search is continued for non-overlapping patches of secondary importance.
ConSSeq / Consensus Sequence
Represents graphically information about amino acid conservation based on sequence alignments reported in homology-derived structures of proteins (HSSP). ConSSeq is a web-based application that allows the user to visualize graphically how each position in the sequence alignment provided by HSSP varies in terms of occupancy by 20 amino acids. It presents the consensus sequence and information about the amino acids, which are predominant at each position of the alignment. ConSSeq is part of the STING Millennium Suite.
FuncPatch
An intuitive web server to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures. Both simulations and four case studies based on empirical data suggest that FuncPatch is a good approximation to GP4Rate. However, FuncPatch is orders of magnitudes faster than GP4Rate. In addition, simulations suggest that FuncPatch is potentially a useful tool complementary to Rate4Site, but the 3D sliding window method is less powerful than FuncPatch and Rate4Site.
JET / Joint Evolutionary Trees
Detects very different types of interactions of a protein with another protein, ligands, DNA, and RNA. JET, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary information. It uses carefully designed sampling method, making sequence analysis more sensitive to the functional and structural importance of individual residues. JET also uses a clustering method parametrized on the target structure for the detection of patches on protein surfaces and their extension into predicted interaction sites.
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