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Fragment Finder
A web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone C[alpha] angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs, STAMP and PROFIT, provided in the server. The freely available Java plug-in Jmol has been interfaced with the server for the visualization of the query and superposed fragments.
RASMOT-3D PRO / Recursive Automatic Search of MOTif in 3D structures of PROteins
Performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology. Comparison is based on Calpha and Cbeta atoms in two steps: inter-atomic distances and RMSD. RASMOT-3D PRO takes in input a PDB file containing the 3D coordinates of the searched motif and provides an interactive list of identified protein structures exhibiting residues of similar topology as the motif searched.
deconSTRUCT
Offers an interface to a protein database search engine, usable for a general purpose detection of similar protein (sub)structures. Initially, it deconstructs the query structure into its secondary structure elements (SSEs) and reassembles the match to the target by requiring a (tunable) degree of similarity in the direction and sequential order of SSEs. Hierarchical organization and judicious use of the information about protein structure enables deconSTRUCT to achieve the sensitivity and specificity of the established search engines at orders of magnitude increased speed, without tying up irretrievably the substructure information in the form of a hash. In a post-processing step, a match on the level of the backbone atoms is constructed. The results presented to the user consist of the list of the matched SSEs, the transformation matrix for rigid superposition of the structures and several ways of visualization, both downloadable and implemented as a web-browser plug-in.
PatternQuery
Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. PatternQuery is a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data.
Fit3D
An easily accessible web application for highly accurate screening of structural motifs in 3D protein data. Such motifs play key roles in clarification of linkage between protein structure and function, which is still a demanding process. Fortunately, the comparison of three-dimensional residue patterns can aid the functional comprehension. However, there is an urgent need for up-to-date and versatile computational resources to search for local similarities. Fit3D bridges the gap between easy usability and highly accurate pattern matching.
PdPDB / Pattern discovery in PDB structures of metalloproteins
Identifies metallocofactor coordinating patterns. PdPDB extracts all the existing patterns associated with the queried metal ion from one or more Protein Data Bank (PDB) entries. The software can also identify patterns pertaining to specific classes of enzymes by aligning the ligand positions, followed by dropping the information pertaining to non-conserved residues. It can be used in a variety of ways to interrogate metal-binding sequence patterns.
GPS-ARM / Group-based Prediction System - Anaphase-promoting complex/cyclosome recognition motif
Calculates prediction of potentially functional D-boxes and KEN-box in anaphase-promoting complex/cyclosome (APC/C) substrates. GPS-ARM can serve as a useful program for experimentalists. Statistical analysis suggested that the provided D-box and KEN-box proteins are significantly enriched in the midbody, centrosome and kinetochore. Taken together, the GPS-ARM and subsequent analyses provide useful information for further experimental manipulation.
MotAn / Motif Analyzer
Offers a web application for performing an automatic detection of structural motifs. MotAn is available as both a web server and a standalone software. The platform is built around two programs: SheeP and ArchiP that permits to compute b-sheets and contacts between sheets and/or helices for then determining β-hairpins, β-meanders, β-helices, greek keys, interlocks, jellyrolls, β-α-β-motifs and β-α-β-helices. Results can be visualized through Jmol application or downloaded.
GYM
Predicts helix-turn-helix motifs. GYM is also able to detect Homeodomain motifs. It uses an efficient screening process that permits to avoid the generation of most infrequent patterns. The tool shows a significantly low number of false positives. It can detect the longer homeodomain motifs in protein sequences and can be modified to detect other motifs. It requires that an approximate length of the motif be known beforehand and that a reasonably large number of motifs are known and have been detected and verified.
pyLemmings / PYthon based Large Margin Multiple Instance learninG Sytem
Implements large margin methods for Multiple Instance Learning (MIL). pyLEMMINGS can be used for linear and locally linear classification and ranking. It was used for three practical bioinformatics problems: (i) localization of the binding site of calmodulin binding proteins, (ii) identification of prion forming domains and (iii) classification of protein amyloidogenic regions. It supports sparse data as well as parallelization for cross-validation and training.
MIRank / Multiple Instance Ranking
Performs ranking in a multiple instance learning setting. MIRank is a machine learning paradigm that has several applications, such as prediction, for a given molecule class of the molecule with the conformation having the highest human immunodeficiency virus (HIV) inhibition efficacy or prediction of the site of metabolism from which a hydrogen atom is abstracted, for a given molecule. The software was tested on datasets that stem from both applications as well as synthetic data.
Wrappy
Reports such indicators as z-score, i.e. the number of standard deviations an observation is above or below the expected mean value. Wrappy is a dehydron calculator plugin for PyMOL. Dehydrons are displayed using red dashes, average wrapped hydrogens bonds are yellow, and over-wrapped hydrogens bonds are green. There are five parameters that the user can change: two of them control the hydrogen bonds detection, two control the dehydron detection and a last allows the user to select which part of system is used to calculate dehydrons. Wrappy can also be known as Dehydron.
PBE / Protein Block Expert
Obsolete
Allows users to perform comparison and analysis for protein structure. PBE offers a platform composed of 10 tools which can accomplish various tasks such as (i) Encode protein structure into PBs sequence; (ii) Compare structure between a pair of proteins using PB description using both local and global alignment algorithms (iii) Mine a databank derived from SCOP, to detect proteins with similar fold (iv) Browse a database of preprocessed PB sequences and pairwise alignments at family and superfamily levels.
ReMUS / Reinforced Merging for Unique Segments
Allows users to identify sequential unique peptide segments in related protein sequences. ReMUS exists in both web application and standalone software. Studied peptide segments can be visualized in three-dimensional images thanks to structural information from the imported protein sequences. In addition, the software can isolate a unique peptide segments from priority lists to determine whether the segments are exposed to the surfaces at their elementary 3D structures.
SCANMOT
Obsolete
Searches for similarities between proteins by simultaneous matching of multiple motifs. SCANMOT is a server that utilizes the occurrence and position of several conserved motifs along a protein sequence. It is possible to search for similar sequences in entire sequence databases using these conserved regions and the spacing as sole restraints. It can also be useful for applications such as the investigation of distant relationships and cross-family evolutionary connections among proteins.
LFMPro / Local Feature Mining in Proteins
Obsolete
Identifies family-specific local sites and their associated features. LFMPro uses feature vectors associated with local neighborhoods to provide a comprehensive sampling of the protein space. The software utilizes a data-mining approach to detect functional sites shared by a family of proteins without requiring prior knowledge of the location or nature of these sites. It was tested on serine protease family of proteins and two binary classification datasets.
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