User:Eric Martz: Difference between revisions
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<br> | <br> | ||
Personal website: [http://martz.molviz.org martz.molviz.org] | Personal website: [http://martz.molviz.org martz.molviz.org] | ||
<br> | <br> | ||
[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations] | [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations] | ||
| Line 95: | Line 93: | ||
*I started a stub for [[Antibody]]. Article later written by [[User:David Canner]] and others. | *I started a stub for [[Antibody]]. Article later written by [[User:David Canner]] and others. | ||
*[[Avian Influenza Neuraminidase, Tamiflu and Relenza]] | *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]] | ||
**[[Proteopedia:Featured SEL/1]] | |||
*[[Drug and peptide transport in humans]] | |||
** [[Proteopedia:Featured EDU/7]] | |||
** [[Proteopedia:Featured EDU/8]] | |||
*[[Flagella, bacterial]] <- [[Flagellum]], [[Flagellar structure]] | *[[Flagella, bacterial]] <- [[Flagellum]], [[Flagellar structure]] | ||
*[[Flagellar filament of bacteria]] | *[[Flagellar filament of bacteria]] | ||
| Line 112: | Line 114: | ||
*[[Recoverin, a calcium-activated myristoyl switch]] | *[[Recoverin, a calcium-activated myristoyl switch]] | ||
*[[Ribosomal A Site Binding Paromomycin: A Morph]] | *[[Ribosomal A Site Binding Paromomycin: A Morph]] | ||
*[[SARS-CoV-2 protein S priming by furin]] | *[[SARS-CoV-2 protein S priming by furin]] | ||
*[[SARS-CoV-2 spike protein fusion transformation]] | **[[Proteopedia:Featured_SEL/5]] | ||
*[[SARS-CoV-2 spike protein mutations]] | *[[SARS-CoV-2 spike protein fusion transformation]] | ||
**[[Proteopedia:Featured_SEL/6]] | |||
*[[SARS-CoV-2 spike protein mutations]] | |||
**[[Proteopedia:Featured_SEL/7]] | |||
*[[Structure of E. coli DnaC helicase loader]] (about a homology model) | *[[Structure of E. coli DnaC helicase loader]] (about a homology model) | ||
*[[SV40 Capsid Simplified]] | *[[SV40 Capsid Simplified]] | ||
*[[Synthetic nanomaterials from standardized protein blocks]] | |||
*[[Thermal motion of peptide]] | *[[Thermal motion of peptide]] | ||
| Line 169: | Line 175: | ||
====A-B==== | ====A-B==== | ||
*[[About Macromolecular Structure]] | *[[About Macromolecular Structure]] | ||
*[[AlphaFold]] | |||
*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold. | |||
*[[AlphaFold]], an introduction and overview. | |||
*[[AlphaFold2 examples from CASP 14]] | *[[AlphaFold2 examples from CASP 14]] | ||
*[[How to predict structures with AlphaFold| | *AlphaFold3: | ||
**[[Converting AlphaFold3 CIF to PDB]] | |||
**[[User:Eric Martz/AlphaFold3 case studies]] | |||
*AlphaFold: [[How to predict structures with AlphaFold|How to predict structures from sequences]] | |||
*AlphaFold: [[FirstGlance/How to get average pLDDT from AlphaFold models|How to get average pLDDT]] | |||
*[[Alternate locations]] (initiated by Wayne Decatur) | *[[Alternate locations]] (initiated by Wayne Decatur) | ||
**[[Alternate locations of backbones]] | |||
*[[Amino Acids]] | *[[Amino Acids]] | ||
*[[Amino acid composition]] | *[[Amino acid composition]] | ||
| Line 193: | Line 209: | ||
**[[User:Eric_Martz/Cavity_Notes]] | **[[User:Eric_Martz/Cavity_Notes]] | ||
*[[Chain]] <- [[Chains]] | *[[Chains and Chain IDs]] <- [[Chain]] <- [[Chains]] | ||
*[[Clashes]] | *[[Clashes]] | ||
*[[Chimera]] | *[[Chimera]] | ||
| Line 212: | Line 228: | ||
*[[Disulfide bond]] | *[[Disulfide bond]] | ||
*[[Domain]] | *[[Domain]] | ||
*[[Drug and peptide transport in humans]] | |||
*[[DRuMS]] | *[[DRuMS]] | ||
*[[Eric Martz's Favorites]] | *[[Eric Martz's Favorites]] | ||
*[[Electron cryomicroscopy]] | *[[Electron cryomicroscopy]] | ||
*[[Electron density maps]] | *[[Electron density maps]] | ||
*[[Electrostatic potential maps]] | |||
** [[Proteopedia:Featured EDU/6]] | |||
*[[Empirical models]] | *[[Empirical models]] | ||
*[[Epitopes]] | *[[Epitopes]] | ||
| Line 235: | Line 254: | ||
*[[History of Macromolecular Visualization]] | *[[History of Macromolecular Visualization]] | ||
*[[Homology modeling]] | *[[Homology modeling]] | ||
*[[How to find a protein's best structure]] | |||
*[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide to]] | *[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide to]] | ||
*[[Homology modeling servers]] | *[[Homology modeling servers]] | ||
| Line 254: | Line 274: | ||
**[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics]] | **[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics]] | ||
*[[Isopeptide bond]] <- [[Isopeptide bonds]] | *[[Isopeptide bond]] <- [[Isopeptide bonds]] | ||
*[[Joining AlphaFold predictions for halves of a molecule]] | |||
*[[Knots in proteins]] | *[[Knots in proteins]] | ||
*[[Ligand]] | *[[Ligand]] | ||
*[[Lysine-cysteine NOS bonds]] <-- [[NOS]] Disambiguation | *[[Lysine-cysteine NOS bonds]] <-- [[NOS]] Disambiguation | ||
*[[Membrane proteins]] | *[[Membrane proteins]] | ||
*[[Missing residues and incomplete sidechains]] | |||
*[[Molecular modeling and visualization software]] | *[[Molecular modeling and visualization software]] | ||
*[[Molecular Playground]] | *[[Molecular Playground]] | ||
| Line 271: | Line 293: | ||
*[[Non-Standard Residues]] | *[[Non-Standard Residues]] | ||
*[[Lysine-cysteine NOS bonds|NOS bonds]] | *[[Lysine-cysteine NOS bonds|NOS bonds]] | ||
*[[Proteopedia:Overview|Overview of Proteopedia]] | |||
*[[PDB identification code]] <- [[PDB code]], [[PDB codes]], [[pdb code]], [[pdb codes]] | *[[PDB identification code]] <- [[PDB code]], [[PDB codes]], [[pdb code]], [[pdb codes]] | ||
*[[Peptide]] (page created by Eran Hodis) | *[[Peptide]] (page created by Eran Hodis) | ||
| Line 283: | Line 306: | ||
**[[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Los cuatro niveles estructurales de las proteínas]] | **[[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Los cuatro niveles estructurales de las proteínas]] | ||
*[[Pyrrolysine]] | *[[Pyrrolysine]] | ||
*[[Quality assessment for molecular models]] | *[[Quality assessment for molecular models]] | ||
*[[R value]] | *[[R value]] | ||
| Line 291: | Line 312: | ||
** See also [[Dihedral/Index]] (initiated by Angel Herráez) | ** See also [[Dihedral/Index]] (initiated by Angel Herráez) | ||
*[[User:Eric Martz/Remarkable Structures|Remarkable Structures]] | *[[User:Eric Martz/Remarkable Structures|Remarkable Structures]] | ||
*[[RMSD]] | |||
*[[Renumbering PDB files]] | *[[Renumbering PDB files]] | ||
*[[Resolution]] | *[[Resolution]] | ||
*[[Retractions and Fraud]] | *[[Retractions and Fraud]] | ||
*[[Ribosomal_A_Site_Binding_Paromomycin:_A_Morph]] | |||
====S-Z==== | ====S-Z==== | ||
| Line 315: | Line 338: | ||
*[[Temperature value vs. resolution]] | *[[Temperature value vs. resolution]] | ||
*[[Temperature color schemes]] | *[[Temperature color schemes]] | ||
*[[Theoretical models]] <- [[Theory]], [[Theoretical model]] | *[[Theoretical models]] <- [[Theory]], [[Theoretical model]] | ||
**[[Proteopedia:Featured_SEL/8]] | |||
*[[Thioester protein cross-links]] | *[[Thioester protein cross-links]] | ||
*[[Thioether protein crosslinks]] | |||
*[[Unusual sequence numbering]] | *[[Unusual sequence numbering]] | ||
*[[Van der Waals radii]] | *[[Van der Waals radii]] | ||
*[[FirstGlance/Virus Capsids and Other Large Assemblies|Virus Capsids and Other Large Assemblies]] | |||
** Polio: [[Proteopedia:Featured EDU/4]] | |||
** Eastern Equine Encephalitis virus [[Proteopedia:Featured EDU/5]] | |||
** Bacterial gas vesicles [[Proteopedia:Featured SEL/9]] | |||
*[[Introduction to molecular visualization|Visualization, molecular, introduction to]] | *[[Introduction to molecular visualization|Visualization, molecular, introduction to]] | ||
*[[Water in macromolecular models]] | *[[Water in macromolecular models]] | ||
| Line 332: | Line 361: | ||
*[[Art:Five Bakers Dancing]] | *[[Art:Five Bakers Dancing]] | ||
*[[History of Macromolecular Visualization]] | *[[History of Macromolecular Visualization]] | ||
*[[Art:Molecular jacks]] | |||
*[[Art:Molecular Sculpture]] | *[[Art:Molecular Sculpture]] | ||
*[[Art:Pentagonal Garden]] | *[[Art:Pentagonal Garden]] | ||
| Line 339: | Line 369: | ||
===Interactive 3D Complements=== | ===Interactive 3D Complements=== | ||
* [[User:Fadel_A._Samatey/FlhBc_I]] (April, 2013) | * [[User:Fadel_A._Samatey/FlhBc_I]] (April, 2013) | ||
* [[User:Fadel A. Samatey/FlgA I]] (June, 2016) | |||
** [[Proteopedia:Featured JRN/1]] | |||
*[[Malvankar/1]] (March, 2015) | *[[Malvankar/1]] (March, 2015) | ||
** Animations of pilus model: [http://proteopedia.org/wiki/images/b/b5/Geobacter_pilus_assembling_animation.gif Assembly], [http://proteopedia.org/wiki/images/0/0f/Geobacter_pilus_assembled_rocking.gif Rocking], [http://proteopedia.org/wiki/images/0/0a/Geobacter_pilus_aromatics_rotating.gif Aromatics]. | ** Animations of pilus model: [http://proteopedia.org/wiki/images/b/b5/Geobacter_pilus_assembling_animation.gif Assembly], [http://proteopedia.org/wiki/images/0/0f/Geobacter_pilus_assembled_rocking.gif Rocking], [http://proteopedia.org/wiki/images/0/0a/Geobacter_pilus_aromatics_rotating.gif Aromatics]. | ||
*[[Malvankar/2]] (April, 2019) | |||
** [[Proteopedia:Featured JRN/3]] | |||
*[[Malvankar/3]] (September, 2021) | |||
** [[Proteopedia:Featured JRN/4]] | |||
*[[Ke Xiao/1]] (March, 2016) | *[[Ke Xiao/1]] (March, 2016) | ||
| Line 389: | Line 425: | ||
*[[PyMOL]] | *[[PyMOL]] | ||
*[[RasMol]] | *[[RasMol]] | ||
*Samson, see [[Sculpting protein conformations]]. | |||
*[[Swiss-PDBViewer = DeepView]] | *[[Swiss-PDBViewer = DeepView]] | ||
**[[DeepView/Mutating Amino Acids]] | **[[DeepView/Mutating Amino Acids]] | ||
| Line 430: | Line 467: | ||
*[[Proteopedia:About]] | *[[Proteopedia:About]] | ||
*[[Proteopedia:Guidelines for Ethical Writing]] was started by Jaime Prilusky. I added the sections on ''Content Attribution'' and ''Images''. | *[[Proteopedia:Guidelines for Ethical Writing]] was started by Jaime Prilusky. I added the sections on ''Content Attribution'' and ''Images''. | ||
*[[User:Eric Martz/Proteopedia:Introduction]] | |||
*[[Proteopedia:Languages]] | *[[Proteopedia:Languages]] | ||
*[[Proteopedia:Namespaces]] | *[[Proteopedia:Namespaces]] | ||
*[[Proteopedia:News]] | *[[Proteopedia:News]] | ||
*[[Proteopedia:Overview]] <- [[Introduction to Proteopedia]] | |||
*[[Proteopedia:Policy]] | *[[Proteopedia:Policy]] | ||
*[[:Proteopedia:Problems]] | *[[:Proteopedia:Problems]] | ||
| Line 452: | Line 491: | ||
===Templates=== | ===Templates=== | ||
To find all templates contributed by a user, at the user's page, click User contributions (at left), then set the namespace to Templates. | |||
*[[Template:Article_under_development]] | *[[Template:Article_under_development]] | ||
*[[Template:Button Toggle Animation]] used at [[Lac repressor]] and [[Template:Button Toggle Animation2]] generally more useful. | *[[Template:Button Toggle Animation]] used at [[Lac repressor]] and [[Template:Button Toggle Animation2]] generally more useful. | ||
| Line 475: | Line 516: | ||
*[[Template:Homology Modeling Intro]] | *[[Template:Homology Modeling Intro]] | ||
*[[Template:Jmol application instructions]] | *[[Template:Jmol application instructions]] | ||
*[[Template:Martz email]] | |||
*[[Template:Molecular Playground animation description]] | *[[Template:Molecular Playground animation description]] | ||
*[[Template:MP masthead]] | |||
*[[Template:Murthy_fraud]] | *[[Template:Murthy_fraud]] | ||
*[[Template:PDBMapViewers]] | *[[Template:PDBMapViewers]] | ||
| Line 486: | Line 529: | ||
*[[Template:Theoretical model]] | *[[Template:Theoretical model]] | ||
*[[Template:Unsigned applets]] | *[[Template:Unsigned applets]] | ||
==Pages by Others That I Especially Like== | ==Pages by Others That I Especially Like== | ||
| Line 573: | Line 613: | ||
*[[User:Eric Martz/Sandbox 3]] '''Miniprotein & microprotein notes''' | *[[User:Eric Martz/Sandbox 3]] '''Miniprotein & microprotein notes''' | ||
*[[User:Eric Martz/Sandbox 4]] Running state scripts for virus capsids and large assemblies | *[[User:Eric Martz/Sandbox 4]] Running state scripts for virus capsids and large assemblies | ||
*[[User:Eric Martz/Sandbox 5]] | *[[User:Eric Martz/Sandbox 5]] Caption tests | ||
*[[User:Eric Martz/Sandbox 6]] H274Y Tamiflu resistance mutation in N1 | *[[User:Eric Martz/Sandbox 6]] H274Y Tamiflu resistance mutation in N1 | ||
*[[User:Eric Martz/Sandbox 7]] PyMOL translator notes | *[[User:Eric Martz/Sandbox 7]] PyMOL translator notes | ||
| Line 586: | Line 626: | ||
*[[User:Eric Martz/Sandbox 16]] PNGJ & caption SAT tests | *[[User:Eric Martz/Sandbox 16]] PNGJ & caption SAT tests | ||
*[[User:Eric Martz/Sandbox 17]] More PNGJ & caption SAT tests | *[[User:Eric Martz/Sandbox 17]] More PNGJ & caption SAT tests | ||
*[[User:Eric Martz/Sandbox 18]] '''Available''' | *[[User:Eric Martz/Sandbox 18]] Saving from SAT removes FILTER command | ||
*[[User:Eric Martz/Sandbox 19]] PACUPP analysis of porin | |||
*[[User:Eric Martz/Sandbox 20]] '''Available''' | |||
*[[User:Eric Martz/Sandbox 21]] '''Available''' | |||
*[[User:Eric Martz/Sandbox 22]] '''Available''' | |||
*[[User:Eric Martz/liveConnect Test]] hyperlink to javascript applet.script(...): HTML not interpreted | *[[User:Eric Martz/liveConnect Test]] hyperlink to javascript applet.script(...): HTML not interpreted | ||
| Line 616: | Line 661: | ||
*[[User:Nikhil Malvankar/Cytochrome nanowires]] <- [[Malvankar/2]] | *[[User:Nikhil Malvankar/Cytochrome nanowires]] <- [[Malvankar/2]] | ||
*[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]] | *[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]] | ||
====Ke Xiao Collaborations==== | ====Ke Xiao Collaborations==== | ||
Latest revision as of 05:25, 6 March 2025
|
| Teaching at Osaka University, Japan, 2009, in Keiichi Namba's Protonic Nanomachine Group. Photograph courtesy of Akihiro Kawamoto.
(See T-shirts below.) |
Professor Emeritus, University of Massachusetts, Amherst MA USA
Personal website: martz.molviz.org
Publications and Citations
((quick link for accts))
Proteopedia Pages to Which I've ContributedProteopedia Pages to Which I've Contributed
Unless otherwise indicated, these are pages that I created, and for which I provided the initial content.
Below, -> or <- mean that one page redirects to another page.
Molecules: Topic PagesMolecules: Topic Pages
- I started a stub for Antibody. Article later written by User:David Canner and others.
- Avian Influenza Neuraminidase, Tamiflu and Relenza
- Drug and peptide transport in humans
- Flagella, bacterial <- Flagellum, Flagellar structure
- Flagellar filament of bacteria
- Flagellar hook of bacteria
- Flaps Morph for HIV Protease
- Gramicidin Channel in Lipid Bilayer
- Influenza hemagglutinin: I started a stub; article later written by User:Savannah Anderson and others.
- Lac repressor
- Lipase lid morph
- Major Histocompatibility Complex Class I
- Mechanosensitive channels: opening and closing included MORPHS
- Membrane proteins
- Metal-Ligand Polyhedra
- Nitrotyrosine
- Nucleosomes: User:Eric Martz/Nucleosomes (a protected page for lectures), which was copied into Nucleosomes so others can improve it.
- Proton Channels, which includes an animated morph.
- Recoverin, a calcium-activated myristoyl switch
- Ribosomal A Site Binding Paromomycin: A Morph
- SARS-CoV-2 protein S priming by furin
- SARS-CoV-2 spike protein fusion transformation
- SARS-CoV-2 spike protein mutations
- Structure of E. coli DnaC helicase loader (about a homology model)
- SV40 Capsid Simplified
- Synthetic nanomaterials from standardized protein blocks
- Thermal motion of peptide
Molecules: PDB Code-Titled PagesMolecules: PDB Code-Titled Pages
- 1hgf Influenza hemagglutinin
- 2ic8 (green links in overview) Author Ya Ha in 2008 believes the BioUnit is a monomer, though in the 2006 publication, they speculated that it was a trimer. The PDB file deems it a monomer.
- 2rd0 Phosphatidylinositol kinase oncogene: I authored scenes similar to many of the figures from the publication.
Topic Pages: Lists of Other PagesTopic Pages: Lists of Other Pages
- About Macromolecular Structure
- High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
- Research Groups and Institutes
- Structural bioinformatics servers
- Student Projects
- Teaching Scenes, Tutorials, and Educators' Pages <- Molecule of the Month, MotM, Motm
- See also Topic pages -> Proteopedia: Topic Pages
Topic Pages - EducationTopic Pages - Education
(Some of these pages are linked redundantly under other headings on this page.)
- Adoptions in College and University Classes
- High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
- Molecular Workbench
- Protein 3D Structure Resources for Educators 2016
- Quizzes
- User:Eric Martz/Antibody Quiz
- User:Eric Martz/Antibody Answers for open-ended questions provided with the Antibody tutorial at MolviZ.Org
- User:Eric Martz/Hemoglobin Quiz
- User:Eric Martz/MHC Quiz
- User:Eric Martz/MHC Answers for open-ended questions provided with the MHC tutorial at MolviZ.Org
- User:Eric Martz/Ramachandran Principle Quiz
- Student Projects
- Teaching Scenes, Tutorials, and Educators' Pages <- Molecule of the Month, MotM, Motm
- Teaching Strategies Using Proteopedia
- Technology-Enhanced Science Activities for STEMEd 6 Mar 2010
- User:Eric Martz/Introduction to Structural Bioinformatics
Topic Pages - Molecular PlaygroundTopic Pages - Molecular Playground
- Molecular Playground/HIV Protease Inhibitor
- Molecular Playground/Relenza
- Molecular Playground/Tamiflu
Topic Pages - Structural BioinformaticsTopic Pages - Structural Bioinformatics
A-BA-B
- AlphaFold/Index, a list of Proteopedia pages about AlphaFold.
- AlphaFold, an introduction and overview.
- AlphaFold2 examples from CASP 14
- AlphaFold3:
- AlphaFold: How to predict structures from sequences
- AlphaFold: How to get average pLDDT
- Alternate locations (initiated by Wayne Decatur)
- Amino Acids
- Amino acid composition
- Asymmetric Unit
- Atomic coordinate file <- PDB file, PDB file format
- Backbone representations
- Biological Unit <- Quaternary structure
- Biological Unit: Showing
- Buried charges detection
C-EC-E
- CASP
- Cation-pi interactions (started by Wayne Decatur)
- Cavities:
- Chains and Chain IDs <- Chain <- Chains
- Clashes
- Chimera
- Conservation, Evolutionary <- Evolutionary Conservation
- ConSurf/Index
- ConSurfDB vs. ConSurf
- CPK
- Crosslinks:
- Cryo-EM
- Crystal contacts
- Cystine
- Density maps
- Disulfide bond
- Domain
- Drug and peptide transport in humans
- DRuMS
- Eric Martz's Favorites
- Electron cryomicroscopy
- Electron density maps
- Electrostatic potential maps
- Empirical models
- Epitopes
- Ester protein crosslinks
- Evolutionary conservation: see Conservation
- Extremophiles
F-HF-H
- Fadel A. Samatey Group also in Japanese
- Favorites
- FirstGlance/Index
- Four levels of protein structure -- Los cuatro niveles estructurales de las proteínas
- Free R
- GDT_TS, calculating
- Header of PDB file
- Hetero atoms
- Highest impact structures of all time.
- Histidine-tyrosine protein crosslinks
- History of Macromolecular Visualization
- Homology modeling
- How to find a protein's best structure
- Homology Modeling, Practical Guide to
- Homology modeling servers
- How to predict structures with AlphaFold
- Hydrogen bonds
- Hydrogen in macromolecular models
I-MI-M
- Improving published models
- Index pages
- Influenza
- Interface analysis servers
- Interpreting ConSurf Results
- Intrinsically Disordered Protein authored largely by User:Tzviya Zeev-Ben-Mordehai
- Introductions to
- Isopeptide bond <- Isopeptide bonds
- Joining AlphaFold predictions for halves of a molecule
- Knots in proteins
- Ligand
- Lysine-cysteine NOS bonds <-- NOS Disambiguation
- Membrane proteins
- Missing residues and incomplete sidechains
- Molecular modeling and visualization software
- Molecular Playground
- Molecular sculpture
- Molecular visualization, introduction to
- Morphs of conformational changes of macromolecules <- Morph
- Multiple Protein Sequence Alignment Display with MSAReveal
N-RN-R
- Nitrotyrosine
- NMR Ensembles of Models <- NMR
- Nobel Prizes for 3D Molecular Structure
- Non-Standard Residues
- NOS bonds
- Overview of Proteopedia
- PDB identification code <- PDB code, PDB codes, pdb code, pdb codes
- Peptide (page created by Eran Hodis)
- Peptide bond <- Peptide bonds
- Personal favorites
- Phi and psi angles
- Post-translational modification <- Post-translational modifications, Posttranslational modification, Posttranslational modifications
- Protein <- Proteins
- Protein crosslinks
- Protein Data Bank <- PDB
- Protein primary, secondary, tertiary and quaternary structure
- Pyrrolysine
- Quality assessment for molecular models
- R value
- Ramachandran principle and phi psi angles (Tutorial) and accompanying Quiz
- Proteopedia:Featured EDU/1
- See also Dihedral/Index (initiated by Angel Herráez)
- Remarkable Structures
- RMSD
- Renumbering PDB files
- Resolution
- Retractions and Fraud
- Ribosomal_A_Site_Binding_Paromomycin:_A_Morph
S-ZS-Z
- Salt bridges
- Sculpting protein conformations
- Sculpture, molecular
- Selenocysteine
- Selenomethionine
- Sequence numbering, unusual
- Sites, Functional
- Standard Residues and Non-Standard Residues
- Structural Bioinformatics, Introduction to aka 565.molviz.org
- Structural bioinformatics servers
- Structural genomics
- Structures_Gallery_Generator
- Structure superposition tools
- Suggestions for new articles
- Superposition tools
- Teaching Strategies Using Proteopedia
- Temperature value <- B value, Disorder, Temperature factor, Temperature
- Temperature value vs. resolution
- Temperature color schemes
- Theoretical models <- Theory, Theoretical model
- Thioester protein cross-links
- Thioether protein crosslinks
- Unusual sequence numbering
- Van der Waals radii
- Virus Capsids and Other Large Assemblies
- Polio: Proteopedia:Featured EDU/4
- Eastern Equine Encephalitis virus Proteopedia:Featured EDU/5
- Bacterial gas vesicles Proteopedia:Featured SEL/9
- Visualization, molecular, introduction to
- Water in macromolecular models
- World Index of BioMolecular Visualization Resources
- X-ray crystallography <- X-ray diffraction
Art, MolecularArt, Molecular
- Category:PDB_Art
- Art:Cytochrome_Wallpaper
- Art:Deconstructing 2GTL
- Art:Dodecapod
- Art:Faberge Eggs
- Art:Five Bakers Dancing
- History of Macromolecular Visualization
- Art:Molecular jacks
- Art:Molecular Sculpture
- Art:Pentagonal Garden
- Art:Rainbow_Corn
- Art:War of the Worlds
Interactive 3D ComplementsInteractive 3D Complements
- User:Fadel_A._Samatey/FlhBc_I (April, 2013)
- User:Fadel A. Samatey/FlgA I (June, 2016)
- Malvankar/1 (March, 2015)
- Malvankar/2 (April, 2019)
- Malvankar/3 (September, 2021)
- Ke Xiao/1 (March, 2016)
- Interactive 3D Complements in Proteopedia (page started by Jaime Prilusky & David Canner) <- I3DC
Topic Pages: People/BiographiesTopic Pages: People/Biographies
SoftwareSoftware
JmolJmol
- Jmol
- Jmol/Index <- About Jmol About JSmol Help:Jmol Help:JSmol
- Jmol/Application
- Jmol/Visualizing large molecules
- Jmol/Visualizing membrane position: lipid bilayer boundaries.
- Jmol/Cavities pockets and tunnels
- Jmol/Depth from surface
- Jmol/PDB file editing with Jmol
- FirstGlance in Jmol
JSmolJSmol
- How JSmol Works and User:Eric Martz/How JSmol works.
- User:Eric Martz/JSmol Notes <--- TABLE OF EXAMPLE SIZES
- JSmol/Rotation Speeds
- using pspeed to maintain tranlucency, see User:Jaime_Prilusky/platformSpeed
FirstGlanceFirstGlance
- FirstGlance/Index lists related resources within Proteopedia and elsewhere.
- FirstGlance Entry Page with links to Purpose, Pros & Cons and YouTube: Design Goals and Quick Introduction.
- About FirstGlance in Jmol
- FirstGlance/Evaluating Protein Crosslinks
Non-JmolNon-Jmol
- CCP4
- Chime
- Java
- Kinemages, Mage and KiNG
- Molecular Workbench
- Protein Explorer
- PyMOL
- RasMol
- Samson, see Sculpting protein conformations.
- Swiss-PDBViewer = DeepView
EMail ListEMail List
Meta PagesMeta Pages
HelpHelp
|
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- Help:Color Keys
- Help:Coloring text
- Help:Copying FirstGlance Scenes into Proteopedia
- Help:Editing
- Help:Getting Started in Proteopedia
- Help:How to Insert a ConSurf Result Into a Proteopedia Green Link
- Help:Language Translation
- Help:Making animations for Powerpoint
- Help:Plain text editors
- Help:Protected Pages
- Help:Quiz
- Help:Sandboxes
- Help:Snapshots
- Help:Uploading molecules
ProteopediaProteopedia
- Mugs and T-Shirts: I created these products and set up the non-profit store at cafepress.com/molviz4.
- News (disambiguation)
- Proteopedia:About
- Proteopedia:Guidelines for Ethical Writing was started by Jaime Prilusky. I added the sections on Content Attribution and Images.
- User:Eric Martz/Proteopedia:Introduction
- Proteopedia:Languages
- Proteopedia:Namespaces
- Proteopedia:News
- Proteopedia:Overview <- Introduction to Proteopedia
- Proteopedia:Policy
- Proteopedia:Problems
- Proteopedia:Scrapbook
- Proteopedia:Subdirectories
- Proteopedia:Supplementary materials
- Proteopedia:Topic Pages
- Proteopedia:What's New <- What's New?, What's New, what's new, What's New in Proteopedia?
- Proteopedia:Wishlist
Proteopedia Pages Using Jmol Color Key LegendsProteopedia Pages Using Jmol Color Key Legends
MediawikiMediawiki
TemplatesTemplates
To find all templates contributed by a user, at the user's page, click User contributions (at left), then set the namespace to Templates.
- Template:Article_under_development
- Template:Button Toggle Animation used at Lac repressor and Template:Button Toggle Animation2 generally more useful.
- Template:Chemical Components
Color KeysColor Keys
- Template:ColorKey_ConSurf
- Template:ColorKey_N2CRainbow
- Example of use: NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia
- The Templates used on the DRuMS and Help:Color Keys pages. All begin "Template:ColorKey".
Green LinksGreen Links
- Template:Green_links_zoom See also adaptation emphasizing rotation of a morph at SARS-CoV-2_protein_S_activation_by_furin
- Template:ClickGreenLinks
- Template:Homology Modeling Intro
- Template:Jmol application instructions
- Template:Martz email
- Template:Molecular Playground animation description
- Template:MP masthead
- Template:Murthy_fraud
- Template:PDBMapViewers
- Template:Possible_fraud
- Template:Protected page banner
- Example of use: User:Karl Oberholser/Ramachandran Plots
- Template:Sandbox Reserved Eric Martz
- Template:Sandbox Reserved Eric Martz 2
- Template:Sandbox Reserved Eric Martz 3
- Template:Theoretical model
- Template:Unsigned applets
Pages by Others That I Especially LikePages by Others That I Especially Like
This is not a complete list -- it is a just a few that I want to be able to find easily in case I forget.
- Ozonolysis
- 2fbw has a comment (correction) by a user, illustrating how a banner alerts users about comments in the discussion tab.
- Proteopedia:Comments on Published Structures
WorkshopsWorkshops
- One-day courses in molecular visualization and structural bioinformatics for researchers and educators.
Principal Author or Architect of (Elsewhere):Principal Author or Architect of (Elsewhere):
- FirstGlance in Jmol, a general-purpose molecular visualization tool which has been adopted by Nature (see the 3D View links), the ConSurf Server, and other journals and structural bioinformatics servers. Available 2005-present.
- Visualization for the the ConSurf Server developed by Nir Ben-Tal, Fabian Glaser, Elana Erez and others, which colors amino acids by evolutionary conservation, completely automatically. Available 2002-present.
- Top Five 3D Molecular Visualization Technologies for the Rest Of Us. Page available 2007-present.
- MolviZ.Org with tutorials in Jmol and molecular visualization resources for educators and students. Included is a DNA Structure Tutorial started in 1996, and now (in collaboration with Angel Herráez) available in 5 languages.
- World Index of BioMolecular Visualization Resources. Available 2000-2012.
- Atlas of Macromolecules. Available 2002-present.
- With Jaime Prilusky, the PDB Lite search interface for students and beginners to find published macromolecular models. Available 1998-2010 (decommisioned).
- An incomplete History of Macromolecular Visualization which includes a list of the earliest macromolecules solved by X-ray crystallography. Available 1997-present.
- molvis-list, founded in 1995 as the RasMol List. Maintained largely by Tim Driscoll/molvisions.com since 2004.
And in an earlier era
- Protein Explorer 1998-present.
- The RasMol Classic Site (formerly the RasMol Home Page) founded 1996. (The current RasMol Home Page is at RasMol.Org by Herbert Bernstein, available since 1999.)
Personal QuicklinksPersonal Quicklinks
HelpHelp
- Special:Prefixindex
- <span style="font-size:150%">Samatey Group</span>
- {{Clear}}
- <table align="right" width="" style="margin: 10px 10px;"><tr><td>[[Image:]]</table></table><tr><td>Caption</td></tr></table>
- [[Image:wiki.png|frame|Wikipedia Encyclopedia]]
- Help:Editing
- Images: Basic Markup / Full Image Syntax
- Tables
- Proteopedia:Cookbook
- Rectangular Jmol
- Image Maps
- Theoretical Model Template
- Floating Quote Box
- Links in Applet Caption
- Flash .swf
- Template:Button_Toggle_Animation
- User:Eric Martz/Getting email from Proteopedia
PDB ExamplesPDB Examples
- Sites (after 2nd remediation): 1uu1 (AC1); 1fws (AC1-6); 1sid (AC1-9, BC1-9, all "binding sites"); 1pop (AC1-AC9, BC1-BC9, CC1-CC6 all "binding sites" + CAT "CAT"); 1zzz (CAT "Active Site");
Files UploadedFiles Uploaded
Sandboxes Reserved for TeachingSandboxes Reserved for Teaching
- Created by Eric: 1-161
- Template:Sandbox Reserved Eric Martz [1-40] 1-10 May-July 2015 Osaka Univ
- Formerly 1-40 May-July 2014 Osaka Univ
- Formerly May-July 2013 Osaka Univ
- Formerly May-July 2012 Osaka Univ
- Formerly May-July 2011 Osaka Univ
- Formerly Apr-Jun 2010 Osaka Univ
- Template:Sandbox Reserved Eric Martz 2 41-100 Jan-Mar 2011 UMass
- Formerly 41-100 Feb-Mar 2010 Israel and extra 151-161
- Template:Sandbox Reserved Eric Martz 3 [101-150] 101-125 May-July 2015 Okinawa Inst Sci Tech, Samatey
- Formerly Oct-Dec 2013 UMass Chem-Bio Interface Thompson
- Formerly May-Jul 2010 UMass
- Template:Sandbox Reserved Eric Martz 4
Sandboxes for CollaborationsSandboxes for Collaborations
- Sandbox Eric Martz (not protected) DeShais Collaboration
- Sandbox2 Eric Martz (not protected) ConSurfDB Collaboration
- Sandbox3 Eric Martz (not protected) (deleted; was Samatey)
- Sandbox4 Eric Martz (not protected) (available)
- Sandbox 5 Eric Martz (not protected) Heme Morph (Prilusky)
- Sandbox6 Eric Martz (not protected) Penghua Wang cas pa se 12
- Sandbox7 Eric Martz (not protected) (available)
Sandboxes: ProtectedSandboxes: Protected
- User:Eric Martz/Sandbox Movie tests
- User:Eric Martz/Sandbox 0 Knots in Proteins - see Methods in Sandbox 11
- User:Eric Martz/Sandbox 2 FGiJ state script -> Proteopedia
- User:Eric Martz/Sandbox 3 Miniprotein & microprotein notes
- User:Eric Martz/Sandbox 4 Running state scripts for virus capsids and large assemblies
- User:Eric Martz/Sandbox 5 Caption tests
- User:Eric Martz/Sandbox 6 H274Y Tamiflu resistance mutation in N1
- User:Eric Martz/Sandbox 7 PyMOL translator notes
- User:Eric Martz/Sandbox 8 Water
- User:Eric Martz/Sandbox 9 Tunnel
- User:Eric Martz/Sandbox 10 hbonds
- User:Eric Martz/Sandbox 11 knot methods
- User:Eric Martz/Sandbox 12 links that perform searches
- User:Eric Martz/Sandbox 13 Sequence Alignment Tools
- User:Eric Martz/Sandbox 14 Jmol 12.2 Tests
- User:Eric Martz/Sandbox 15 Ramachandran references
- User:Eric Martz/Sandbox 16 PNGJ & caption SAT tests
- User:Eric Martz/Sandbox 17 More PNGJ & caption SAT tests
- User:Eric Martz/Sandbox 18 Saving from SAT removes FILTER command
- User:Eric Martz/Sandbox 19 PACUPP analysis of porin
- User:Eric Martz/Sandbox 20 Available
- User:Eric Martz/Sandbox 21 Available
- User:Eric Martz/Sandbox 22 Available
- User:Eric Martz/liveConnect Test hyperlink to javascript applet.script(...): HTML not interpreted
WorkbenchesWorkbenches
- All Eric Martz Workbenches (search using Prefixindex)
- User:Eric Martz/Workbench/AccountManagement
- User:Eric Martz/Workbench tests
- User:Eric Martz/Workbench/Workbench01
- User:Eric Martz/Workbench 02 is for testing read access to users given permission.
CollaborationsCollaborations
SamateySamatey
- Samatey
- Fadel_A._Samatey_Group
- User:Fadel A. Samatey has links to Samatey Workbenches
- User:Fadel_A._Samatey/FlhBc_I <- Samatey/1 was not used in Acta Cryst D paper.
- User:Fadel_A._Samatey/FlgA_I <- Samatey/2 linked in paper in SciRep.
- User:Fadel A. Samatey/FlgE I <- Samatey/3 linked in paper in SciRep.
- User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure <- Samatey/4 linked in paper in NatComm.
- File:3b0z-all-chain-a.pdb.gz
Malvankar CollaborationsMalvankar Collaborations
- User:Nikhil Malvankar
- Malvankar
- User:Nikhil Malvankar/Geobacter pilus <- Malvankar/1
- User:Nikhil Malvankar/Cytochrome nanowires <- Malvankar/2
- User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function <- Malvankar/3
Ke Xiao CollaborationsKe Xiao Collaborations
Protected Topic PagesProtected Topic Pages
- User:Eric Martz/Cavities tests
- User:Eric Martz/Entertaining PDB codes (amusing, humor)
- User:Eric Martz/Remarkable Structures
- User:Eric Martz/Nucleosomes (cf. Nucleosomes)
- User:Eric Martz/Introduction to Structural Bioinformatics and 2012
- User:Eric Martz/Virus capsid resources
- User:Eric Martz/Molecular Playground/Tamiflu
- User:Eric Martz/Molecular Playground/HIVDrug
- User:Eric Martz/Molecular Playground/Authoring
- User:Eric Martz/5eon cf. pili
All Protected PagesAll Protected Pages
Other QuicklinksOther Quicklinks
Personal To Do ListPersonal To Do List
- Knots
Pages Needing RepairsPages Needing Repairs
- Lac repressor some scenes broken
- Structural alignment tools: the morph green link hangs JSmol (2/2021) but morph green links work on other pages (tested: Lac repressor, recovering, mechanosensitive, avian influ.)