About Macromolecular Structure: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| (22 intermediate revisions by the same user 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: | ||
**[[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 25: | 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 44: | 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]] | |||
*[[Ester protein crosslinks]] [[Image:New yellow1.gif]] | *[[Ester protein crosslinks]] [[Image:New yellow1.gif]] | ||
*[[Extremophiles]] | *[[Extremophiles]] | ||
| Line 59: | 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 68: | 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 81: | 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 100: | Line 110: | ||
*[[Quality assessment for molecular models]] | *[[Quality assessment for molecular models]] | ||
*[[R value]] | *[[R value]] | ||
*[[Ramachandran Plots]] | |||
*[[Renumbering PDB files]] | |||
*[[Resolution]] | *[[Resolution]] | ||
*[[Retractions and Fraud]] | *[[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]] | ||
*[[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 alignment tools]] | ||
*[[Structural annotation]] | *[[Structural annotation]] | ||
| Line 120: | Line 131: | ||
*[[Structural bioinformatics servers]] | *[[Structural bioinformatics servers]] | ||
*[[Structural genomics]] | *[[Structural genomics]] | ||
*[[Structures Gallery Generator]] | |||
*[[Structure superposition tools]] | |||
*[[Suggestions for new articles]] | *[[Suggestions for new articles]] | ||
*[[Teaching Strategies Using Proteopedia]] | *[[Teaching Strategies Using Proteopedia]] | ||
| Line 126: | 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]] | ||
