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Dali server
A network service for comparing protein structures in 3D. Dali server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user.
A web service for efficient protein structural similarity searches. iSARST gives tables listing co-linear or circularly permuted homologs of the query proteins and a functional summary of the best hits. Superimposed structures can be examined through an interactive and informative visualization tool. It can be used for both co-linear homologs and circular permutants, and serves as a rapid annotation system for functionally unknown or hypothetical proteins, which are increasing rapidly in this post-genomics era.
ProteinDBS / Protein DataBase Search engine
Applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. ProteinDBS is a web server for the life science community to search for similar protein tertiary structures in real time. It applies advanced feature extraction algorithms and scalable indexing techniques to achieve a high-running speed while preserving reasonably high precision of structural comparison.
Searches the protein data bank, for similar chains, calculates structural alignments and generates a list of structurally related proteins. SALAMI has the advantage that it relies on chain connectivity and has no problem finding similarities when there are hinge-bending or domain motions. The graduated similarity measures mean that poor quality structures and deviations from regular geometry are well treated. Finally, the alignment method is very tolerant of large gaps and insertions, and tends to produce slightly longer alignments than other similar programs.
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.
GOSSIP / GlObal Structural SuperposItion of Proteins
Detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. GOSSIP provides a useful means for performing fast and accurate analysis of large datasets of protein structures.
Reduces a protein to a series of secondary structure elements (SSEs) and adds information to the SSE descriptors such as relative direction, accessibility, adjacency to the previous SSE, length and length of preceding loop. TOPSCAN is a method for comparing protein structures. It is useful as a preliminary screen to give some idea whether a protein looks like something else. It trades coverage (and to some degree error rate) for great speed. For more accurate comparisons, a method which works at the detailed coordinate level such as SSAP need to be used.
Possesses several unique features that positively affect computational efficiency of the system. The most important characteristics of HDInsight4Psi are: the use of sequence files, possible elimination of the Reduce phase, and location of the MapReduce computations in the Azure cloud, which allows an on-demand scaling. HDInsight4PSi was also faster than its predecessor Cloud4Psi. Moreover, HDInsight4PSi system with the implemented parallel procedure for similarity searching can be easily scaled in the Cloud, both vertically and horizontally, in order to handle the dynamic growth of macromolecular data.
Cloud4Psi / Cloud for Protein Similarity
Enables researchers to search for protein structure similarities by using a combination of three algorithms: jCE, jFATCAT-rigid and jFATCAT-flexible. Cloud4Psi allows for the completion of the task much faster by distributing computation on many machines. It is a highly scalable and high-performance solution for protein similarity searching and function identification. Cloud4Psi was developed for use in the Microsoft Azure public cloud.
pvSOAR / pocket and void Surfaces Of Amino acid Residues
Recognizes similar surface regions in three-dimensional protein structures. pvSOAR compares local sequences, local shapes and local orientations between residues located on a geometrically defined pocket or void. It equally confronts a query pattern of surface sequence and substructure with a database of patterns from known protein structures. This tool offers search methods to users to query against several specialized protein surface databases.
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