Table of Contents for Model Analysis Applications

Special Category: Volume and Packing Calculations

Special Category: Questions and Methods for Every New Structure

3DNA : Nucleic acid structure analysis and visualization
ACCESS : Surface Accessibility
APROPOS: Calculate pockets on the surface of a molecule
ASC: Analytic Surface Calculation
AutoDock:Program for the Automated Docking of Flexible Ligands to Macromolecules
AQUA: Check Geometry in NMR Protein Structures
CCP4 Program Suite : Structure Refinement
CHI:Computational searching of protein helix interactions
CNS: Crystallography and NMR System (Local Only)
CoordComp: Compare Side Chain Movements
CURVES: Helical Analysis of Irregular Nucleic Acids
DALI Server Comparing protein structures in 3D
DEFINE_S : Secondary Structure Analysis and Plot
DELPHI: Calculate Charge Distribution
Difference Distance Matrix Plot (DDMP) : Compare C-alpha positions
Dials and Windows : Display of DNA structure and MD simulations
DialX : Dials plots from X-PLOR trajectories
DOCK: Most Favorable Ligand/Receptor Binding
DSSP Program : Secondary Structure Calculation
DSSP Database Secondary Structure Assignments
FREEHELIX: Analysis of radically bent and kinked DNA
gnuplot: Function plotting program
GRASP: Calculate surface areas
HBPLUS: Hydrogen Bond Calculation
HELANAL: A program to characterize overall geometry of an alpha helix.
HOLE: Analyze pores and channels
LIGPLOT : 2D schematic diagrams of protein-ligand interactions
MOLEMAN2: Manipulation and analysis of PDB files
MSMS: Solevent Excluded Surface and Volume Calculation
MSP: Molecular Surface Package : Surfaces and Volumes
OS: Occluded Surface : Packing Analysis
PROCHECK: Check Geometry in Crystal Protein Structures
PROCHECK-NMR: Check Geometry in NMR Protein Structures
PROFILE : Eisenberg 3D Environment Analysis
PyMOL : Molecular Graphics and Animations
ROTAMER : Side Chain Rotamer Analysis
SPOCK: Molecular Graphics
Structural Classification of Proteins Families, Superfamilies and Folds
SURFNET: Surface Gaps, Clefts and Voids
SurfVol: Mark Gerstein's Surface Area and Volume Programs
Swiss-PDBViewer: Friendly interface to analyse several proteins at the same time
Uppsala Software Factory: Gerard Kleywegt's Programs
VOIDOO: Cavity and volume calculation, surface generation
VOLUME : Residue Voronoi Volumes
WHAT_IF: CHECK Residue environments
Xmgr : X, Y Plotting and Regression
Xplor : Structure Refinement