About Macromolecular Structure
From Proteopedia
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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. | 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. | ||
| - | [[Image:New yellow1.gif]] means the article first became available in Proteopedia | + | [[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/Index]] [[Image:New yellow1.gif]] has a list of pages in Proteopedia about AlphaFold, including: | ||
| + | **[[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]] | ||
*[[Anisotropic refinement]] | *[[Anisotropic refinement]] | ||
*[[Asymmetric Unit]] | *[[Asymmetric Unit]] | ||
*[[Atomic coordinate file|Atomic Coordinate File]] | *[[Atomic coordinate file|Atomic Coordinate File]] | ||
| + | *[[Backbone representations]] | ||
*[[Believe It or Not]] | *[[Believe It or Not]] | ||
*[[Biological process]] | *[[Biological process]] | ||
*[[Biological Unit]] | *[[Biological Unit]] | ||
| - | *[[CASP]] Biannual '''C'''ritical '''A'''ssessment of protein '''S'''tructure '''P'''rediction | + | *[[Buried charges detection]] [[Image:New yellow1.gif]] |
| + | *[[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*]][[Image:New yellow1.gif]] | + | *[[CC*]], an alternative to the R value [[Image:New yellow1.gif]] |
| + | *[[Chain]] | ||
| + | *[[Clashes]] [[Image:New yellow1.gif]] | ||
*[[Classes of globular proteins]] | *[[Classes of globular proteins]] | ||
| + | *[[Cryo-EM|Cryo-electron microscopy]] [[Image:New yellow1.gif]] | ||
*[[Cystine]] | *[[Cystine]] | ||
*[[Conservation, Evolutionary]] | *[[Conservation, Evolutionary]] | ||
| + | *[[CPK|Corey-Pauling-Koltun]] | ||
| + | *[[CPK]] | ||
| + | *[[Crystal contacts]] | ||
*[[Introduction to Evolutionary Conservation|Conservation, Evolutionary, Introduction to]] | *[[Introduction to Evolutionary Conservation|Conservation, Evolutionary, Introduction to]] | ||
*[[Disulfide bond]] | *[[Disulfide bond]] | ||
*[[Domain|Domain, protein]] | *[[Domain|Domain, protein]] | ||
| + | *[[DRuMS]] | ||
| + | *[[Electron cryomicroscopy]] [[Image:New yellow1.gif]] | ||
| + | *[[Electron density maps]] has [[Image:New yellow1.gif]] illustrations. | ||
| + | *[[Electrostatic potential maps]] [[Image:New yellow1.gif]] | ||
| + | *[[Empirical models]] [[Image:New yellow1.gif]] | ||
| + | *[[Ester protein crosslinks]] [[Image:New yellow1.gif]] | ||
*[[Extremophiles]] | *[[Extremophiles]] | ||
| + | *[[Favorites]] | ||
*[[Free R]] | *[[Free R]] | ||
*[[Function]] | *[[Function]] | ||
| Line 41: | Line 62: | ||
*[[Forms of DNA|Helices in DNA]] compares A-, B- and Z- | *[[Forms of DNA|Helices in DNA]] compares A-, B- and Z- | ||
*[[Helices in Proteins]] compares alpha, pi and 3-10 | *[[Helices in Proteins]] compares alpha, pi and 3-10 | ||
| + | *[[Hetero atoms]] | ||
*[[Highest impact structures]] | *[[Highest impact structures]] | ||
| - | *[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide | + | *[[Histidine-tyrosine protein crosslinks]] [[Image:New yellow1.gif]] |
| + | *[[History of Macromolecular Visualization]] | ||
| + | *[[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 50: | Line 75: | ||
*[[Interface analysis servers]] | *[[Interface analysis servers]] | ||
*[[Intrinsically Disordered Protein]] | *[[Intrinsically Disordered Protein]] | ||
| + | *[[Introduction to molecular visualization]] [[Image:New yellow1.gif]] | ||
| + | *[[Isopeptide bond]] with [[Image:New yellow1.gif]] illustrations. A type of [[Protein crosslinks|protein crosslink]]. | ||
*[[Ligand]] | *[[Ligand]] | ||
| + | *[[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]] | ||
*[[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 60: | Line 91: | ||
*[[Nitrotyrosine]] | *[[Nitrotyrosine]] | ||
*[[NMR Ensembles of Models]] | *[[NMR Ensembles of Models]] | ||
| + | *[[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]]) | ||
*[[Peptide]] | *[[Peptide]] | ||
| + | *[[Peptide bond]] | ||
*[[Personal favorites]] | *[[Personal favorites]] | ||
*[[PDB file format]] | *[[PDB file format]] | ||
*[[PDB identification code]] | *[[PDB identification code]] | ||
| - | *[[Practical Guide to Homology Modeling]] [[ | + | *[[Post-translational modification]] |
| + | *[[Practical Guide to Homology Modeling]] | ||
| + | *[[Protein]] | ||
*[[Protein Data Bank]] | *[[Protein Data Bank]] | ||
| - | *[[ | + | *[[Protein crosslinks]] [[Image:New yellow1.gif]] |
| + | *[[Protein primary, secondary, tertiary and quaternary structure]] [[Image:New yellow1.gif]] | ||
| + | *[[Protein primary, secondary, tertiary and quaternary structure (Spanish)]] [[Image:New yellow1.gif]] | ||
| + | *[[Pseudoenzyme]] | ||
*[[Pyrrolysine]], sometimes called the 22nd amino acid | *[[Pyrrolysine]], sometimes called the 22nd amino acid | ||
*[[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]] | ||
*[[Selenocysteine]], the 21st amino acid | *[[Selenocysteine]], the 21st amino acid | ||
| + | *[[Selenomethionine]] | ||
| + | *[[Unusual sequence numbering|Sequence numbering, unusual]] | ||
*[[Single protein]] | *[[Single protein]] | ||
*[[Sites|Sites, Functional]] | *[[Sites|Sites, Functional]] | ||
*[[Molecular modeling and visualization software|Software for molecular modeling and visualization]] | *[[Molecular modeling and visualization software|Software for molecular modeling and visualization]] | ||
*[[Standard Residues]] (see also [[Non-Standard Residues]]) | *[[Standard Residues]] (see also [[Non-Standard Residues]]) | ||
| + | *[[Structural alignment tools]] | ||
*[[Structural annotation]] | *[[Structural annotation]] | ||
| + | *[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics, Introduction to]] | ||
*[[Structural bioinformatics servers]] | *[[Structural bioinformatics servers]] | ||
*[[Structural genomics]] | *[[Structural genomics]] | ||
| + | *[[Structures Gallery Generator]] | ||
| + | *[[Structure superposition tools]] | ||
| + | *[[Suggestions for new articles]] | ||
*[[Teaching Strategies Using Proteopedia]] | *[[Teaching Strategies Using Proteopedia]] | ||
*[[Temperature value]] | *[[Temperature value]] | ||
| + | *[[Theoretical models]] has [[Image:New yellow1.gif]] coverage of the 2020 AlphaFold breakthrough. | ||
| + | *[[Thioester 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
