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--- comparative_modelling [2016/02/26 11:15]
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+++ comparative_modelling [2021/09/24 13:03] (actual)
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@@ Línea 1: / Línea 1: @@
-==== On line services ====
+==== Comparative Modelling ====
-[[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://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
+[[https://predictioncenter.org/ | CASP:]] Critical Assessment of Techniques for Protein Structure Prediction
+=== On line ===
+[[https://www.rosettacommons.org/software/ | Rosetta:]]The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
+[[https://yanglab.nankai.edu.cn/trRosetta/ | trRosetta]] is an algorithm for fast and accurate protein structure prediction. It builds the protein structure based on direct energy minimizations with a restrained Rosetta. The restraints include inter-residue distance and orientation distributions, predicted by a deep neural network. Homologous templates are included in the network prediction to improve the accuracy further.
+[[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###
+[[https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 | Multicom:]] MULTICOM2 open‑source protein structure prediction system powered by deep learning and distance prediction
+[[https://www.alphafold.ebi.ac.uk/ | AlphaFold:]] Protein Structure Database
+[[http://feig.bch.msu.edu/web/research/protein-structure-refinement/ | FEIG:]] Protein structure refinement
+[[https://toolkit.tuebingen.mpg.de/#/tools/hhpred | HHpred - Homology detection:]] useful for select an appropriate template for protein structure modelling###
+[[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.sbg.bio.ic.ac.uk/~phyre2/ | PHYRE2:]] Protein Homology/analogY Recognition Engine V 2.0. MULTIPLE TEMPLATE
@@ Línea 14: / Línea 35: @@
 [[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://www.proteinmodelportal.org/?pid=modelling_interactive | The protein Model portal:]] Interactive Modeling
+== Ab-initio method ==
@@ Línea 26: / Línea 50: @@
 [[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 ====
+== Local software ==
 [[http://salilab.org/modeller/modeller.html | MODELLER:]] is used for homology or comparative modeling of protein three-dimensional structures
@@ Línea 38: / Línea 65: @@
-==== LINKS to other servers ====
+=== PDB file manipulator ===
+[[https://github.com/pandegroup/pdbfixer | pdb fixer]]
+[[http://lorentz.dynstr.pasteur.fr/pdb/index.php | PDB Fixer]]
+[[https://pitgroup.org/decomp/ | Decomp:]] The PDB Structural Decomposition Tool repairs and decomposes files from the Protein Data Bank PDB formats.
+==== LINKS to other servers ====
 [[http://salilab.org/bioinformatics_resources.html | Programs and World Wide Web servers]] useful in comparative modeling (Laboratory Andrej Sali)

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