Richards Center at Yale University
RC Home | Search | Table of Contents | General Information

Last Modified: Friday, 17-Oct-2008 11:16:52 EDT

Data Reduction and Analysis Applications

ACCESS : Surface Accessibility
APROPOS : Calculate pockets on the surface of a molecule
ARP:Automated Refinement Procedure
AutoDock:Automated Docking of Flexible Lig ands to Macromolecules
ASC: Analytic Surface Calculation
AQUA: Check Geometry in NMR Protein Structures

BABEL: File conversion

CCP4 Program Suite : Structure Refinement
CHI:Computational searching of protein helix interactions
CNS: Crystallography and NMR System (Local Only)
COORDCOMP: All atom difference distance plot
CRITXPL: Plotting of R and Rfree, Etot, BOND, ANGL, DIHE, VDW, NOE, etc.
CURVES: Helical Analysis of Irregular Nucleic Acids

Difference Distance Matrix Plot : Compare C-alpha positions
DEFINE_S : Secondary Structure Analysis and Plot
DELPHI: Calculate Charge Distribution
DEMON/ANGEL: Density Modification and Averaging
DENZO : Diffraction Data Reduction
Dials and Windows : Display of DNA structure and MD simulations
DOCK: Most Favorable Ligand/Receptor Binding
DPS_GUI: Process Quantum-4 CCD Detector Data
DSSP Program : Secondary Structure Calculation
d*TREK: Diffraction Data Reduction

FREEHELIX: Analysis of radically bent and kinked DNA

gnuplot: Function plotting program
Grace: X,Y Plotting and Regression
GVX: Greg Van Duyne's Programs

HBPLUS: Hydrogen Bond Calculation
HEAVY: Heavy Atom Search and Refinement

MATHEMATICA: Doing Mathematics by Computer
MATLAB: Alternative Doing Mathematics by Computer
MADSYS: Multi-wavelength Anomalous Diffraction Refinement
MAXSCALE : Scaling Fhkl's
MODELLER : Protein Homology and Comparative Modeling
Mosflm : Processing of rotation data collected on either image plate or film.
MSMS: Solvent Excluded Surface and Volume Calculation
MSP: Molecular Surface Package : Surfaces and Volumes

Newlsc : Local Scaling Program Developed by Alan Friedman at the Yale CSB.
NMRPipe : Fourier processing, display and analysis of NMR spectra
NMRView : Visualization and analysis of NMR datasets
Nuclin-Nuclsq: A rapid and automatic online refinement tool of partial or full assemblies of nucleic acids

OS: Occluded Surface : Packing Analysis

PATTERN: Display Diffraction Pattern
PDB Validation Suite: Validation of 3D structure data
Phaser : Maximum Likelihood Phasing
PHASES : Computing Phase Angles
PHENIX : Automated crystal structure determination
PROCHECK: Check Geometry in Crystal Protein Structures
PROCHECK-NMR: Check Geometry in NMR Protein Structures
PROFILE : Eisenberg 3D Environment Analysis
RAVE : Density Averaging
Replace: Rotational and translational searches of unit cells
RESOLVE: Maximum-likelihood density modification

SHARP: Statistical Heavy- Atom Refinement and Phasing
SHELX : Structure Refinement
SIMS: Computation of a smooth invariant molecular surface
SnB: Normalize and visualize x-ray crystal structures
SOLVE: Crystallographic structure solution for MIR and MAD
Sparky: Assign and intergrate peaks in NMR spectra
SurfVolume: Mark Gerstein's surface area and volume programs

TNT: Refinement by Least Squares Function-minimization

Uppsala Software Factory: Gerard Kleywegt's programs

VOLUME : Residue Voronoi Volumes
VNMR : NMR data acquisition, processing and display

Westhof Programs:RNA refinement and modeling package

XDS : X-ray Detector Software for processing troublesome diffraction data
XDS (Antique version): Data Streamer for the obsolete Xentronics Area Detector
Xmgr : X, Y Plotting and Regression
Xplor : Structure Refinement
XWPL and WPLIB: Wavelet Packets Analysis

Last Modified: Friday, 17-Oct-2008 11:16:52 EDT

RC Home | Search | Table of Contents | General Information
Richards Center ( at Yale University (
Contact: webmaster_at_ben^rc^yale^edu