Bioinformatics Tools

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==== On line services ==== [[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ | I-TASSER server:]] is an on-line platform for protein structure and function predictions. 3D models are built based on multiple-threading alignments by LOMETS and iterative template fragment assembly simulations; function inslights are derived by matching the 3D models with BioLiP protein function database. I-TASSER (as 'Zhang-Server') was ranked as the No 1 server for protein structure prediction in recent CASP7, CASP8, CASP9, and CASP10 experiments [[http://raptorx.uchicago.edu/ | RaptorX]] is a protein structure prediction server. excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). MULTIPLE TEMPLATE [[http://www.sbg.bio.ic.ac.uk/~phyre2/ | PHYRE2:]] Protein Homology/analogY Recognition Engine V 2.0. MULTIPLE TEMPLATE [[http://swissmodel.expasy.org//SWISS-MODEL.html | SwissModel:]] An Automated Comparative Protein Modelling Server [[http://modbase.compbio.ucsf.edu/ModWeb20-html/modweb.html | Mod Web:]] Server for Comparative Protein Structure Modeling.(Modeller) [[http://www.bmm.icnet.uk/servers/3djigsaw/ | 3D-JIGSAW]] Protein Comparative Modelling Server [[http://www.cbs.dtu.dk/services/CPHmodels/ | CPHmodels-2.0 Server]] [[http://www.sbg.bio.ic.ac.uk/~phyre/ | PHYRE:]] Protein Homology/analogY Recognition Engine ==== Ab-initio method ==== [[http://robetta.bakerlab.org/ | Robetta:]] The Rosetta method attempts to predict protein structure from sequence without the aid of a homologous sequence or structure [[http://mordred.bioc.cam.ac.uk/~rapper/ | RAPPER:]] is an ab initio conformational search algorithm for restraint-based protein modelling [[http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD/ | PEP-FOLD]] is a de novo approach aimed at predicting peptide structures from amino acid sequences. This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field ==== local software ==== [[http://salilab.org/modeller/modeller.html | MODELLER:]] is used for homology or comparative modeling of protein three-dimensional structures [[https://www.schrodinger.com/ | schrodinger:]]Schrödinger is the scientific leader in computational chemistry, providing software solutions and services for life sciences and materials research [[http://www.bio.net/bionet/mm/bio-soft/2000-October/023008.html | PSIPRED2]] [[http://www.moldiscovery.com/soft_grid.php | GRID:]] Programme GRID is a computational procedure for determining energetically favourable binding sites on molecules of known structure. [[http://csi.chemie.tu-darmstadt.de/ak/immel/molarch/index.html | MolArch+]] ==== LINKS to other servers ==== [[http://salilab.org/bioinformatics_resources.html | Programs and World Wide Web servers]] useful in comparative modeling (Laboratory Andrej Sali)