About Macromolecular Structure
From Proteopedia
(Difference between revisions)
(→A-F) |
(→S-Z) |
||
| (19 intermediate revisions not shown.) | |||
| Line 11: | Line 11: | ||
[[Image:New yellow1.gif]] means the article first became available in Proteopedia "recently", or that substantial new content was added "recently". See also [[What's New?]]. | [[Image:New yellow1.gif]] means the article first became available in Proteopedia "recently", or that substantial new content was added "recently". See also [[What's New?]]. | ||
==A-F== | ==A-F== | ||
| - | *[[3D Molecular Models | + | *[[3D Molecular Models]] |
*[[Activity]] | *[[Activity]] | ||
| - | *[[AlphaFold]] [[Image:New yellow1.gif]] | + | *[[AlphaFold/Index]] [[Image:New yellow1.gif]] has a list of pages in Proteopedia about AlphaFold, including: |
| - | *[[How to predict structures with AlphaFold|AlphaFold, How To Predict Structures With]] [[Image:New yellow1.gif]] | + | **[[AlphaFold]] [[Image:New yellow1.gif]] |
| + | **[[How to predict structures with AlphaFold|AlphaFold, How To Predict Structures With]] [[Image:New yellow1.gif]] | ||
| + | **[[AlphaFold2 examples from CASP 14]] [[Image:New yellow1.gif]] | ||
*[[Alternate locations]] | *[[Alternate locations]] | ||
*[[Structural alignment tools|Alignment, structural]] | *[[Structural alignment tools|Alignment, structural]] | ||
*[[Amino Acids]] | *[[Amino Acids]] | ||
| - | *[[Amino acid composition | + | *[[Amino acid composition]] |
*[[Anisotropic refinement]] | *[[Anisotropic refinement]] | ||
*[[Asymmetric Unit]] | *[[Asymmetric Unit]] | ||
| Line 26: | Line 28: | ||
*[[Biological process]] | *[[Biological process]] | ||
*[[Biological Unit]] | *[[Biological Unit]] | ||
| + | *[[Buried charges detection]] [[Image:New yellow1.gif]] | ||
*[[CASP]] Biannual '''C'''ritical '''A'''ssessment of protein '''S'''tructure '''P'''rediction | *[[CASP]] Biannual '''C'''ritical '''A'''ssessment of protein '''S'''tructure '''P'''rediction | ||
*[[Cation-pi interactions]] | *[[Cation-pi interactions]] | ||
| + | *[[Calculating GDT_TS]], the global distance test total score, used in [[CASP]] | ||
*[[Cellular component]] | *[[Cellular component]] | ||
*[[CC*]], an alternative to the R value [[Image:New yellow1.gif]] | *[[CC*]], an alternative to the R value [[Image:New yellow1.gif]] | ||
| Line 45: | Line 49: | ||
*[[Electron cryomicroscopy]] [[Image:New yellow1.gif]] | *[[Electron cryomicroscopy]] [[Image:New yellow1.gif]] | ||
*[[Electron density maps]] has [[Image:New yellow1.gif]] illustrations. | *[[Electron density maps]] has [[Image:New yellow1.gif]] illustrations. | ||
| + | *[[Electrostatic potential maps]] [[Image:New yellow1.gif]] | ||
*[[Empirical models]] [[Image:New yellow1.gif]] | *[[Empirical models]] [[Image:New yellow1.gif]] | ||
*[[Ester protein crosslinks]] [[Image:New yellow1.gif]] | *[[Ester protein crosslinks]] [[Image:New yellow1.gif]] | ||
| Line 61: | Line 66: | ||
*[[Histidine-tyrosine protein crosslinks]] [[Image:New yellow1.gif]] | *[[Histidine-tyrosine protein crosslinks]] [[Image:New yellow1.gif]] | ||
*[[History of Macromolecular Visualization]] | *[[History of Macromolecular Visualization]] | ||
| - | *[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide | + | *[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide]] |
*[[Homology modeling]] | *[[Homology modeling]] | ||
*[[Homology modeling servers]] | *[[Homology modeling servers]] | ||
| + | *[[How To Find A Structure]] [[Image:New yellow1.gif]] | ||
*[[Hydrogen bonds]] | *[[Hydrogen bonds]] | ||
*[[Hydrogen in macromolecular models]] | *[[Hydrogen in macromolecular models]] | ||
| Line 70: | Line 76: | ||
*[[Intrinsically Disordered Protein]] | *[[Intrinsically Disordered Protein]] | ||
*[[Introduction to molecular visualization]] [[Image:New yellow1.gif]] | *[[Introduction to molecular visualization]] [[Image:New yellow1.gif]] | ||
| - | *[[Isopeptide bond]] with [[Image:New yellow1.gif]] illustrations. | + | *[[Isopeptide bond]] with [[Image:New yellow1.gif]] illustrations. A type of [[Protein crosslinks|protein crosslink]]. |
*[[Ligand]] | *[[Ligand]] | ||
| - | *[[Lysine-cysteine NOS bonds]] [[Image:New yellow1.gif]] | + | *[[Lysine-cysteine NOS bonds]], a type of [[Protein crosslinks|protein crosslink]]. [[Image:New yellow1.gif]] |
*[[Maximum Occurrence]] | *[[Maximum Occurrence]] | ||
*[[Jmol/Visualizing membrane position|Membrane position, visualizing]] [[Image:New yellow1.gif]] | *[[Jmol/Visualizing membrane position|Membrane position, visualizing]] [[Image:New yellow1.gif]] | ||
*[[Membrane proteins]] | *[[Membrane proteins]] | ||
| + | *[[Missing residues and incomplete sidechains]] [[Image:New_yellow1.gif]] | ||
*[[Molecular function]] | *[[Molecular function]] | ||
*[[Molecular modeling and visualization software]] | *[[Molecular modeling and visualization software]] | ||
| + | *[[Introduction to molecular visualization|Molecular visualization, introduction to]] | ||
*[[Morphs]] of conformational changes of macromolecules | *[[Morphs]] of conformational changes of macromolecules | ||
| Line 83: | Line 91: | ||
*[[Nitrotyrosine]] | *[[Nitrotyrosine]] | ||
*[[NMR Ensembles of Models]] | *[[NMR Ensembles of Models]] | ||
| - | *[[Non-covalent interactions | + | *[[Non-covalent interactions]] |
*[[Nobel Prizes for 3D Molecular Structure]] | *[[Nobel Prizes for 3D Molecular Structure]] | ||
*[[Non-Standard Residues]] (see also [[Standard Residues]]) | *[[Non-Standard Residues]] (see also [[Standard Residues]]) | ||
| Line 102: | Line 110: | ||
*[[Quality assessment for molecular models]] | *[[Quality assessment for molecular models]] | ||
*[[R value]] | *[[R value]] | ||
| - | *[[Resolution]] | ||
| - | *[[Retractions and Fraud]] [[Image:New_yellow1.gif]] | ||
*[[Ramachandran Plots]] | *[[Ramachandran Plots]] | ||
| + | *[[Renumbering PDB files]] | ||
| + | *[[Resolution]] | ||
| + | *[[Retractions and Fraud]] | ||
| + | *[[RMSD]] [[Image:New_yellow1.gif]] | ||
==S-Z== | ==S-Z== | ||
*[[Salt bridges]] | *[[Salt bridges]] | ||
| - | *[[Sculpting protein conformations | + | *[[Sculpting protein conformations]] |
*[[Selenocysteine]], the 21st amino acid | *[[Selenocysteine]], the 21st amino acid | ||
*[[Selenomethionine]] | *[[Selenomethionine]] | ||
| - | *[[Unusual sequence numbering|Sequence numbering, unusual | + | *[[Unusual sequence numbering|Sequence numbering, unusual]] |
*[[Single protein]] | *[[Single protein]] | ||
*[[Sites|Sites, Functional]] | *[[Sites|Sites, Functional]] | ||
| Line 129: | Line 139: | ||
*[[Thioester protein crosslinks]] [[Image:New yellow1.gif]] | *[[Thioester protein crosslinks]] [[Image:New yellow1.gif]] | ||
*[[Thioether protein crosslinks]] [[Image:New yellow1.gif]] | *[[Thioether protein crosslinks]] [[Image:New yellow1.gif]] | ||
| + | *[[Unknown amino acids and nucleic residues]] [[Image:New yellow1.gif]] | ||
| + | *[[Water in macromolecular models]] | ||
*[[X-ray crystallography]] | *[[X-ray crystallography]] | ||
Current revision
|
For pages about specific molecules or families of molecules, see Proteopedia:Topic Pages. See also Teaching Strategies Using Proteopedia, and the lists of pages under Research Groups and Institutes and Teaching Scenes, Tutorials, and Educators' Pages. For pages about Proteopedia, its contents, policies, implementation, and credits, see Proteopedia:About. |
Below is a list of pages about macromolecular structure topics. This list excludes pages about specific molecules or families of molecules, and pages in the lists linked in the box at right.
means the article first became available in Proteopedia "recently", or that substantial new content was added "recently". See also What's New?.
Contents |
A-F
- 3D Molecular Models
- Activity
- AlphaFold/Index
has a list of pages in Proteopedia about AlphaFold, including:
- Alternate locations
- Alignment, structural
- Amino Acids
- Amino acid composition
- Anisotropic refinement
- Asymmetric Unit
- Atomic Coordinate File
- Backbone representations
- Believe It or Not
- Biological process
- Biological Unit
- Buried charges detection
- CASP Biannual Critical Assessment of protein Structure Prediction
- Cation-pi interactions
- Calculating GDT_TS, the global distance test total score, used in CASP
- Cellular component
- CC*, an alternative to the R value
- Chain
- Clashes
- Classes of globular proteins
- Cryo-electron microscopy
- Cystine
- Conservation, Evolutionary
- Corey-Pauling-Koltun
- CPK
- Crystal contacts
- Conservation, Evolutionary, Introduction to
- Disulfide bond
- Domain, protein
- DRuMS
- Electron cryomicroscopy
- Electron density maps has illustrations.
- Electrostatic potential maps
- Empirical models
- Ester protein crosslinks
- Extremophiles
- Favorites
- Free R
- Function
- Functional annotation
G-M
- Gene
- Helices in DNA compares A-, B- and Z-
- Helices in Proteins compares alpha, pi and 3-10
- Hetero atoms
- Highest impact structures
- Histidine-tyrosine protein crosslinks
- History of Macromolecular Visualization
- Homology Modeling, Practical Guide
- Homology modeling
- Homology modeling servers
- How To Find A Structure
- Hydrogen bonds
- Hydrogen in macromolecular models
- Improving published models
- Interface analysis servers
- Intrinsically Disordered Protein
- Introduction to molecular visualization
- Isopeptide bond with illustrations. A type of protein crosslink.
- Ligand
- Lysine-cysteine NOS bonds, a type of protein crosslink.
- Maximum Occurrence
- Membrane position, visualizing
- Membrane proteins
- Missing residues and incomplete sidechains
- Molecular function
- Molecular modeling and visualization software
- Molecular visualization, introduction to
- Morphs of conformational changes of macromolecules
N-R
- Nitrotyrosine
- NMR Ensembles of Models
- Non-covalent interactions
- Nobel Prizes for 3D Molecular Structure
- Non-Standard Residues (see also Standard Residues)
- Peptide
- Peptide bond
- Personal favorites
- PDB file format
- PDB identification code
- Post-translational modification
- Practical Guide to Homology Modeling
- Protein
- Protein Data Bank
- Protein crosslinks
- Protein primary, secondary, tertiary and quaternary structure
- Protein primary, secondary, tertiary and quaternary structure (Spanish)
- Pseudoenzyme
- Pyrrolysine, sometimes called the 22nd amino acid
- Quality assessment for molecular models
- R value
- Ramachandran Plots
- Renumbering PDB files
- Resolution
- Retractions and Fraud
- RMSD
S-Z
- Salt bridges
- Sculpting protein conformations
- Selenocysteine, the 21st amino acid
- Selenomethionine
- Sequence numbering, unusual
- Single protein
- Sites, Functional
- Software for molecular modeling and visualization
- Standard Residues (see also Non-Standard Residues)
- Structural alignment tools
- Structural annotation
- Structural Bioinformatics, Introduction to
- Structural bioinformatics servers
- Structural genomics
- Structures Gallery Generator
- Structure superposition tools
- Suggestions for new articles
- Teaching Strategies Using Proteopedia
- Temperature value
- Theoretical models has coverage of the 2020 AlphaFold breakthrough.
- Thioester protein crosslinks
- Thioether protein crosslinks
- Unknown amino acids and nucleic residues
- Water in macromolecular models
- X-ray crystallography
Proteopedia Page Contributors and Editors (what is this?)
Eric Martz, Wayne Decatur, Joel L. Sussman, Alejandro Porto, Angel Herraez, Eran Hodis
