Difference between revisions of "Protein structure"
From Christoph's Personal Wiki
| Line 1: | Line 1: | ||
==Topics== | ==Topics== | ||
| − | + | ===[[wikipedia:Protein structure|Protein structure]]=== | |
| + | *[[wikipedia:CATH]] | ||
| + | *[[DSSP]] / [[wikipedia:DSSP (protein)|DSSP]] | ||
| + | *[[wikipedia:Intermolecular force]] | ||
| + | ===Surface=== | ||
*[[wikipedia:Surface area]] | *[[wikipedia:Surface area]] | ||
*[[wikipedia:Accessible surface area]] (ASA; sometimes called the Lee-Richards molecular surface) | *[[wikipedia:Accessible surface area]] (ASA; sometimes called the Lee-Richards molecular surface) | ||
| Line 6: | Line 10: | ||
*[[wikipedia:Van der Waals radius]] | *[[wikipedia:Van der Waals radius]] | ||
*Cavities => internal packing defects | *Cavities => internal packing defects | ||
| − | + | ===Packing efficiency=== | |
| − | + | *[[wikipedia:Sphere packing]] | |
| − | + | *[http://mathworld.wolfram.com/CirclePacking.html Circle Packing] | |
| − | + | *[http://mathworld.wolfram.com/Tessellation.html Tessellation] | |
| − | + | *[http://departments.kings.edu/chemlab/animation/packgeo.html Packing and Geometry] | |
| − | *[[wikipedia: | + | ===Shapes=== |
| − | * | + | *[[wikipedia:Spheroid]] |
| + | *[[wikipedia:Gaussian curvature]] | ||
==External links== | ==External links== | ||
| Line 19: | Line 24: | ||
*[http://www.molmovdb.org/cgi-bin/3v.cgi 3V: Voss Volume Voxelator] — contact volume calculator | *[http://www.molmovdb.org/cgi-bin/3v.cgi 3V: Voss Volume Voxelator] — contact volume calculator | ||
*[http://dirac.cnrs-orleans.fr/MMTK/ The Molecular Modelling Toolkit] | *[http://dirac.cnrs-orleans.fr/MMTK/ The Molecular Modelling Toolkit] | ||
| + | *[http://pauli.utmb.edu/cgi-bin/get_a_form.tcl GETAREA] — Solvent Accessible Surface Areas, Atomic Solvation Energies, and Their Gradients for Macromolecules | ||
| + | *[http://www.csb.yale.edu/userguides/datamanip/os/ Occluded Surface (OS)] | ||
| + | *[http://bioportal.weizmann.ac.il/dipol/dipol.html Web Server to Calculate Dipole Moments of Proteins] | ||
| + | *[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/protein_contact_map/ Protein Contact Maps using BioPython] | ||
| + | *[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/matrix_contour/ Contour Plots of Matrix Data] | ||
| + | *[http://depts.washington.edu/bakerpg/contact_order/ Determine a Protein's Contact Order] | ||
| + | *[http://www.ccp4.ac.uk/html/contact.html CONTACT] ([[CCP4]]) | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
Latest revision as of 02:16, 18 July 2007
Contents
Topics
Protein structure
Surface
- wikipedia:Surface area
- wikipedia:Accessible surface area (ASA; sometimes called the Lee-Richards molecular surface)
- solvent-excluded surface (SES; also known as the molecular surface or Connolly surface)
- wikipedia:Van der Waals radius
- Cavities => internal packing defects
Packing efficiency
Shapes
External links
- Database of Macromolecular Movements
- Macromolecular Geometry
- 3V: Voss Volume Voxelator — contact volume calculator
- The Molecular Modelling Toolkit
- GETAREA — Solvent Accessible Surface Areas, Atomic Solvation Energies, and Their Gradients for Macromolecules
- Occluded Surface (OS)
- Web Server to Calculate Dipole Moments of Proteins
- Protein Contact Maps using BioPython
- Contour Plots of Matrix Data
- Determine a Protein's Contact Order
- CONTACT (CCP4)
