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SA-Search: a web tool for protein structure mining based on a Structural Alphabet

F. Guyon, A.-C. Camproux, J. Hochez, P. Tuffery
2004 Nucleic Acids Research  
SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities.  ...  It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of threedimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited  ...  One strong point of SA-Search is that it allows the fast mining of protein structures, a typical run being on the order of a few seconds.  ... 
doi:10.1093/nar/gkh467 pmid:15215446 pmcid:PMC441605 fatcat:vzd4lgrd5jaqld4buv7v5iaq3i

iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G. de Brevern
2019 Source Code for Biology and Medicine  
Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone.  ...  Proteins are described using PB from which we have previously developed a sequence alignment procedure based on dynamic programming with a dedicated PB Substitution Matrix.  ...  All authors approved the final manuscript for publication.  ... 
doi:10.1186/s13029-019-0075-3 pmid:31700529 pmcid:PMC6825713 fatcat:x3dqoo4osvdf5ckpjeior5xgiq

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

M. Tyagi, P. Sharma, C. S. Swamy, F. Cadet, N. Srinivasan, A. G. de Brevern, B. Offmann
2006 Nucleic Acids Research  
PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs.  ...  PBE-ALIGNc performs structure comparison between two protein structures based on the alignment of their corresponding PB sequences.  ...  Its concept is related to SA-Search (18) web server, but differs greatly as it uses a genuine SA substitution matrix derived on the basis of aligned homologous proteins present in the large Phylogeny  ... 
doi:10.1093/nar/gkl199 pmid:16844973 pmcid:PMC1538797 fatcat:4yatkshxmbfzlhgpc75a75gzym

A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications

Manoj Tyagi, Venkataraman S. Gowri, Narayanaswamy Srinivasan, Alexandre G. de Brevern, Bernard Offmann
2006 Proteins: Structure, Function, and Bioinformatics  
Analysis of protein structures based on backbone structural patterns known as structural alphabets have been shown to be very useful.  ...  Here, for the first time, substitution probabilities of PBs in a large number of aligned homologous protein structures has been studied and is expressed as a simplified 16x16 substitution matrix.  ...  Sairam Swamy for providing the code for dynamic programming and Rajesh Thangudu for his suggestions on the work. NS is an International Senior Fellow of the Wellcome Trust, London.  ... 
doi:10.1002/prot.21087 pmid:16894618 fatcat:fdsjyuez7vdb3j3cmq3332of2u

Local Protein Structures

Bernard Offmann, Manoj Tyagi, Akexandre de Brevern
2007 Current Bioinformatics  
The Structural alphabets section shows firstly the structural libraries dedicated to the structure approximation, secondly the different developed prediction methods based on structural alphabet description  ...  A given complete set of prototypes defines a "structural alphabet." Different groups described these local protein structures according to different criteria.  ...  SA-Search is a web tool developed by Guyon and co-workers (see Figure (14) ) that can be used to mine for proteins with similar fold and extract structural similarities [369] .  ... 
doi:10.2174/157489307781662105 fatcat:wosaroff5jhcnojc7zlozpvd5e

Special Issue: Grid, Cloud and Sky Applications for Knowledge-based Industries and Businesses

Vlado Stankovski, Dana Petcu, Anton Železnikar, Matjaž Gams, Jožef Stefan, Drago Torkar, Jožef Stefan, Juan Carlos, Augusto, Argentina, Costin Badica, Romania (+11 others)
2013 unpublished
Since the available literature on how to implement cloud-based biometric services is extremely scarce, this paper capitalizes on the most important challenges encountered during the development work on  ...  In the final part of the paper, a case study on fingerprint recognition in the cloud and its integration into the e-learning environment Moodle is presented.  ...  The insights provided by Vedat Coskun and Kerem Ok on the earlier versions of the manuscript were fruitful to establish the basis of this research.  ...