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comparative_modelling
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| Ambos lados, revisión anterior Revisión previa Próxima revisión | Revisión previa | ||
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comparative_modelling [2018/01/26 12:54] marenas [LINKS to other servers] |
comparative_modelling [2021/09/24 13:03] (actual) marenas |
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| ==== Comparative Modelling ==== | ==== Comparative Modelling ==== | ||
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| + | [[https://predictioncenter.org/ | CASP:]] Critical Assessment of Techniques for Protein Structure Prediction | ||
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| === On line === | === On line === | ||
| + | [[https://www.rosettacommons.org/software/ | Rosetta:]]The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. | ||
| - | [[https://toolkit.tuebingen.mpg.de/#/tools/hhpred | HHpred - Homology detection:]] useful for select an appropriate template for protein structure modelling### | + | [[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://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### | [[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://www.sbg.bio.ic.ac.uk/~phyre2/ | PHYRE2:]] Protein Homology/analogY Recognition Engine V 2.0. MULTIPLE TEMPLATE | + | [[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 |
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| + | [[https://www.alphafold.ebi.ac.uk/ | AlphaFold:]] Protein Structure Database | ||
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| + | [[http://feig.bch.msu.edu/web/research/protein-structure-refinement/ | FEIG:]] Protein structure refinement | ||
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| + | [[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://swissmodel.expasy.org//SWISS-MODEL.html | SwissModel:]] An Automated Comparative Protein Modelling Server | [[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://modbase.compbio.ucsf.edu/ModWeb20-html/modweb.html | Mod Web:]] Server for Comparative Protein Structure Modeling.(Modeller) | ||
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| + | [[http://www.sbg.bio.ic.ac.uk/~phyre2/ | PHYRE2:]] Protein Homology/analogY Recognition Engine V 2.0. MULTIPLE TEMPLATE | ||
| Línea 23: | Línea 38: | ||
| [[http://www.sbg.bio.ic.ac.uk/~phyre/ | PHYRE:]] Protein Homology/analogY Recognition Engine | [[http://www.sbg.bio.ic.ac.uk/~phyre/ | PHYRE:]] Protein Homology/analogY Recognition Engine | ||
| - | [[https://www.rosettacommons.org/software/ | Rosetta:]]The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. | ||
| [[http://www.proteinmodelportal.org/?pid=modelling_interactive | The protein Model portal:]] Interactive Modeling | [[http://www.proteinmodelportal.org/?pid=modelling_interactive | The protein Model portal:]] Interactive Modeling | ||
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| == Ab-initio method == | == Ab-initio method == | ||
| Línea 35: | 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 | [[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 | ||
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| == Local software == | == Local software == | ||
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| - | == PDB file manipulator == | + | === PDB file manipulator === |
| [[https://github.com/pandegroup/pdbfixer | pdb fixer]] | [[https://github.com/pandegroup/pdbfixer | pdb fixer]] | ||
comparative_modelling.1516982043.txt.gz · Última modificación: 2018/01/26 12:54 por marenas
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