User:Angel Herraez
From Proteopedia
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| + | Angel Herráez, PhD - Dept. of Systems Biology; | ||
| + | Biochemistry and Molecular Biology Unit; | ||
| + | [http://www.uah.es/ University of Alcalá], Spain | ||
| + | == Personal == | ||
| + | Not much info here, but you can visit | ||
| + | * my website, 'Biomodel' with [http://biomodel.uah.es educational materials] (also [http://biomodel.uah.es/en/ in English] and other languages). | ||
| + | * [http://biomodel.uah.es/personal personal page] with some details, papers, congresses, courses... related to Molecular Visualization | ||
| + | * [http://wiki.jmol.org:81/index.php/User:AngelHerraez my page in the Jmol Wiki] | ||
| + | * [[Proteopedia:Development|Proteopedia developments]] | ||
| - | [[User:Angel Herraez/Sandbox 1]] | + | == Favourite pages == |
| + | * [[Helices in Proteins]] comparing alpha, pi and 3-10 helices in parallel. | ||
| + | * [[Forms of DNA]] comparing A-, B- and Z- helices of DNA | ||
| + | * Two-slide summary on the 4 levels of protein structure, made by Eric Martz, [[Four_levels_of_protein_structure|in English]] <ref>[[User:Eric_Martz|Martz, Eric]] (2016) [https://docs.google.com/presentation/d/1lS59hde5F6ur9VCBO1_eHwXbhQcUHByPPVi12w6PSRM/edit?usp=sharing "Four Levels of Protein Structure"]. Accessed on 14 February 2016.</ref> and [[Four_levels_of_protein_structure_%28Spanish%29|in Spanish]] <ref>[[User:Eric_Martz|Martz, Eric]] (2016) [https://docs.google.com/presentation/d/1xCx8OTWusFeEzEpe9UuxtRrIjO6843HSujB1GYu97Ro/edit?usp=sharing "Los cuatro niveles estructurales de las proteínas - Four Levels of Protein Structure (Spanish)"]. Accessed on 14 February 2016.</ref> | ||
| + | |||
| + | === Tutorials === | ||
| + | * [[User:Angel Herraez/Sandbox Advanced Scenes|Advanced Scenes]] (importing external states into a scene) -- pending relocation | ||
| + | * [[Proteopedia:Cookbook]] | ||
| + | * [[Tutorial:Basic_Chemistry_Topics]] | ||
| + | |||
| + | == Academic pages == | ||
| + | Pages produced by my students. | ||
| + | |||
| + | === TFG === | ||
| + | (Trabajos de Fin de Grado) End-of-degree projects focused of the analysis and display of structural features of proteins, interaction with ligands, etc. | ||
| + | * [[User:Carlos_V%C3%A1zquez_Garc%C3%ADa/TFG|Carlos Vázquez-García]]. 2016, on the '''K-Ras''' protein. 6 ECTS credits, Degree in Pharmacy. http://hdl.handle.net/10017/27238 | ||
| + | * [[User:Carolina_Castro_Hern%C3%A1ndez/TFG|Carolina Castro-Hernández]]. 2016, on '''gp120 and gp41''', envelope proteins of HIV. 12 ECTS credits, Degree in Biology. | ||
| + | * [[User:María Sánchez Morán/TFG|María Sánchez-Morán]]. 2022, on water photolysis and '''the oxygen-evolving complex''' in photosystem II. 6 ECTS credits, Degree in Chemistry. | ||
| + | * [[User:Clara_Fernández_Vidal/Isocitrato_deshidrogenasa|Clara Fernández-Vidal]]. 2024, on '''isocitrate dehydrogenase''' as a model to demonstrate the use of 3D scenes as rich media for better understanding of structure-function relationships, generating both Proteopedia pages and 3D models embedded in PDF documents. 6 ECTS credits, external internship, Degree in Biomedicine from Universidad Francisco de Vitoria. | ||
| + | |||
| + | == Test pages == | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 1]] - Test for the sequence widget | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 2]] - Testing some templates | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 3]] - Alternate rendering for display of both evolutionary conservation and allosteric site | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 4]] - Test for drag and drop | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 5]] - Misc. testing | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 6]] - Testing advanced scenes imported from Jmol application via state file | ||
| + | |||
| + | [[User:Angel Herraez/Sandbox 7]] - Testing proposals for ligand focus | ||
| + | |||
| + | [[User:Angel Herraez/Workbench]] - for private work | ||
| + | |||
| + | |||
| + | This [https://proteopedia.org/cgi-bin/getSampleStructures page] provides information on model features (nr. of models, MW, CA/P only, experimental method) from an internal database in Proteopedia. | ||
| + | (Note: you must be logged in Proteopedia) | ||
| + | |||
| + | This [https://proteopedia.org/cgi-bin/infopdb?1crn page] retrieves from PDBe useful information about a structure (only Calpha & P, number of models, molecular weights, experimental method); change the pdb ID in the url. | ||
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{{STRUCTURE_3cin | PDB=3cin | SCENE= }} | {{STRUCTURE_3cin | PDB=3cin | SCENE= }} | ||
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| + | == References == | ||
| + | <references/> | ||
Current revision
Angel Herráez, PhD - Dept. of Systems Biology; Biochemistry and Molecular Biology Unit; University of Alcalá, Spain
Contents |
Personal
Not much info here, but you can visit
- my website, 'Biomodel' with educational materials (also in English and other languages).
- personal page with some details, papers, congresses, courses... related to Molecular Visualization
- my page in the Jmol Wiki
- Proteopedia developments
Favourite pages
- Helices in Proteins comparing alpha, pi and 3-10 helices in parallel.
- Forms of DNA comparing A-, B- and Z- helices of DNA
- Two-slide summary on the 4 levels of protein structure, made by Eric Martz, in English [1] and in Spanish [2]
Tutorials
- Advanced Scenes (importing external states into a scene) -- pending relocation
- Proteopedia:Cookbook
- Tutorial:Basic_Chemistry_Topics
Academic pages
Pages produced by my students.
TFG
(Trabajos de Fin de Grado) End-of-degree projects focused of the analysis and display of structural features of proteins, interaction with ligands, etc.
- Carlos Vázquez-García. 2016, on the K-Ras protein. 6 ECTS credits, Degree in Pharmacy. http://hdl.handle.net/10017/27238
- Carolina Castro-Hernández. 2016, on gp120 and gp41, envelope proteins of HIV. 12 ECTS credits, Degree in Biology.
- María Sánchez-Morán. 2022, on water photolysis and the oxygen-evolving complex in photosystem II. 6 ECTS credits, Degree in Chemistry.
- Clara Fernández-Vidal. 2024, on isocitrate dehydrogenase as a model to demonstrate the use of 3D scenes as rich media for better understanding of structure-function relationships, generating both Proteopedia pages and 3D models embedded in PDF documents. 6 ECTS credits, external internship, Degree in Biomedicine from Universidad Francisco de Vitoria.
Test pages
User:Angel Herraez/Sandbox 1 - Test for the sequence widget
User:Angel Herraez/Sandbox 2 - Testing some templates
User:Angel Herraez/Sandbox 3 - Alternate rendering for display of both evolutionary conservation and allosteric site
User:Angel Herraez/Sandbox 4 - Test for drag and drop
User:Angel Herraez/Sandbox 5 - Misc. testing
User:Angel Herraez/Sandbox 6 - Testing advanced scenes imported from Jmol application via state file
User:Angel Herraez/Sandbox 7 - Testing proposals for ligand focus
User:Angel Herraez/Workbench - for private work
This page provides information on model features (nr. of models, MW, CA/P only, experimental method) from an internal database in Proteopedia.
(Note: you must be logged in Proteopedia)
This page retrieves from PDBe useful information about a structure (only Calpha & P, number of models, molecular weights, experimental method); change the pdb ID in the url.
References
- ↑ Martz, Eric (2016) "Four Levels of Protein Structure". Accessed on 14 February 2016.
- ↑ Martz, Eric (2016) "Los cuatro niveles estructurales de las proteínas - Four Levels of Protein Structure (Spanish)". Accessed on 14 February 2016.
