ACCESS : Surface Accessibility
Adobe Acrobat Reader
alscript :ALignment -> postSCRIPT
ARP:Automated Refinement Procedure
AutoDock:Automated Docking of Flexible Ligands to Macromolecules
APROPOS : Calculate pockets on the surface of a molecule
AQUA: Check Geometry in NMR Protein Structures
ASC: Analytic Surface Calculation
Authoring WWW Documents

BABEL: File conversion
Backup
Basic UNIX
Batch Queing
Biology Workbench Point and click web interface to databases and analysis tools
BLAST : Fully gapped alignment searching
Bobscript:Added functionality to Molscript
Brookhaven Protein Databank
Brunger Lab

Top of Page

Cambridge Structural Data Base Small molecules
CCP4 Program Suite : Structure Refinement
CE : Combinatorial Extension Finds 3D Similarities
CHI:Computational searching of protein helix interactions
Chimera:Interactive visualization and analysis of molecular structures and related data
CLRpaint
Cn3D
CNS: Crystallography and NMR System (Local Only)
Coot: Model Building, Model Completion, and Validation
CoordComp: Compare Side Chain Movements
Core Resources Map
(A) CRITXPL: Plotting of R and Rfree, Etot, BOND, ANGL, DIHE, VDW, NOE, etc.
CSB Computing Policy
CSB General Information
CSB Seminars
CSB Staff
CURVES: Helical Analysis of Irregular Nucleic Acids
Top of Page

DALI Server Comparing protein structures in 3D
Data Bases
Data Collection: Local X-ray generator and Synchrotron Information
Data Reduction and Analysis
(A) 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
(A) DialX
Difference Distance Matrix Plot : Compare C-alpha positions
Disk Use and File Systems
DOCK: Most Favorable Ligand/Receptor Binding
Doudna Lab
(A) DRAWNA: Fast Rendering of 3-D Lighted, Solid Models of Nucleic Acids
DSC: Protein Secondary Structure Prediction
DSSP Program and Database Secondary Structure Assignments
(A) DPS_GUI: Process Quantum-4 CCD Detector Data
d*TREK: Diffraction Data Reduction
Top of Page

Email
Engelman Lab
Entrez Protein, Nucleotide Databases and MEDLINE subset
Explorer

(A) -- FASTA : Sequence Comparison and Searching
FIT2D : 1- and 2-Dimensional Data Analysis
(A) -- FrameMaker: General Document Preparation
(A) -- Fragment:A tool to extract or replace DNA/RNA fragments
(A) -- FREEHELIX: Analysis of radically bent and kinked DNA
FTP Server
Top of Page

GenBank NIH genetic sequence database, RETRIEVE, BLAST
GETENTRY: Retrieval of PDB files.
Ghostscript and Ghostview
GIMP: Photo Retouching, Image Composition and Image Authoring
glrf: See Replace
Gnuplot : Command-driven interactive function and data plotting program.
Grace: X, Y Plotting and Regression (Xmgr replacement)
Grasp
Gaussian
GROMACS: Molecular Dynamics
(A) -- GVX: Greg Van Duyne's Programs

HBPLUS: Hydrogen Bond Calculation
HEAVY: Heavy Atom Search and Refinement
HELANAL: A program to characterize overall geometry of an alpha helix.
HKL2000 : Graphical user interface for the HKL data processing suite.
(A) -- HMMER: Searching with Hidden Markov models
(A) -- HOLE: Analyze pores and channels
How to make Animated GIF Images
How to make surfaces., ribbons, ball-and-stick, electron-density and stick, anisotropic ellipsoid figures.
How to view a protein molecule quickly from a PDB file.
html2ps : File format converter
Top of Page

Image Display and Capture
ImageMagick
Imtools
IRIS Explorer
ISIS/DRAW : Chemical Structure Drawing Package

jot Editor: SGI Text Editor

LIGPLOT : 2D schematic diagrams of protein-ligand interactions
Lynx: WWW Text Browser for Terminal Display
Top of Page

MAIN
Making Slides and Pictures
man2html : File format converter
(A) -- Manip:An interactive tool for modelling RNA
MATHEMATICA: Doing Mathematics by Computer
(A) -- MAXSCALE : Scaling Fhkl's
MGLTools: ADT, PMV, ViPer
MidasPlus
MODELLER : Protein Homology and Comparative Modeling
Molecular Graphics
MOLEMAN2: Manipulation and analysis of PDB files
MOLMOL
Moloc
Molscript
Mosflm: Processing of rotation data collected on either image plate or film.
MSMS: Solevent Excluded Surface and Volume Calculation
MSP: Molecular Surface Package : Surfaces and Volumes
MSV:Molecular Surface Viewer
Moore Lab
Mounting a UNIX directory on a MacIntosh
Moviemaker: For SGI's
Top of Page

NAMD
(A) -- NAMOT
NAOMI
National Library of Medicine
NMRPipe : Fourier processing, display and analysis of NMR spectra
NMRView : Visualization and analysis of NMR datasets
NEdit: Text Editor
newlsc : Local Scaling Program Developed by Alan Friedman at the Yale CSB.
NDB : Nucleic Acid Database at Rutgers
(A) -- Nuclin-Nuclsq: A rapid and automatic online refinement tool of partial or full assemblies of nucleic acids.
Nucplot: Generates schematic 2D representations of protein-nucleic acid interactions

O
Ortep-III: Crystal structure illustration
OS: Occluded Surface and Packing Analysis
Top of Page

PATTERN: Display Diffraction Pattern
Paul Sigler symposium
pdb2vrml
pdb_extract: Conversion of PDB and reflection data into mmCIF Format
PDB Validation Suite: Validation of 3D structure data
People
Phaser: Maximum likelihood Phasing
(A) -- PHASES : Computing Phase Angles
PHENIX : Automated crystal structure determination
Photoshop
PLATON : SHELX97-compatible multipurpose crystallographic tool
PLUTON : Anisotropic B Factor Display
Post-structure Analysis : Questions to ask about every new structure
POV-Ray
Povscript
Practices and Policies
Printers
Printing Supplies: Ordering Paper, Transparencies, Ink Cartridges
PROCHECK: Check Geometry in Crystal Protein Structures
PROCHECK-NMR: Check Geometry in NMR Protein Structures
PROFILE : Eisenberg 3D Environment Analysis
Protein-Protein Interfaces All interfaces with >9 residues interacting
PyMOL : Molecular Graphics and Animations

Top of Page

Quanta -- Molecular graphics
Queen of Spades (Qs) -- Molecular Replacement
Quotas

RasMol
Raster-3D
RAVE : Density Averaging
Rayscript
Rayshade
REDUCE: Build Hydrogens on your Model
Replace: Rotational and translational searches of unit cells
Reserving Work Stations
Ribbons
Richards Lab
RNAView : Quickly generate display of RNA/DNA secondary structures with tertiary interactions
ROSETTA : Prediction and design of protein structures, folding, and interactions
(A) -- ROTAMER : Side Chain Rotamer Analysis
(A) -- RSRef2000 : Real Space module for CNS

SAXS -- Small Angle Xray Scattering
SCOP : Structural Classification of Proteins
(A) -- SETOR
Setting Up your UNIX environment
SgInfo - Space group information
SHARP: Statistical Heavy-Atom Refinement and Phasing
SHELX : Structure Refinement
Sims
Signup: Reserve Instruments or Rooms at CSB
SnB: Normalize and visualize x-ray crystal structures
SOMoRe: Search and Optimization for Molecular Replacement
SOLVE: Crystallographic structure solution for MIR and MAD
Sparky: Assign and intergrate peaks in NMR spectra
SPOCK: Molecular Graphics
Steitz Lab
Structural Classification of Proteins Families, Superfamilies and Folds
SURFNET: Surface Gaps, Clefts and Voids
(A) -- SurfVol: Mark Gerstein's Prgrams to Analyse Protein Geometry
Swiss-PDBViewer: Friendly interface to analyse several proteins at the same time
Synchrotron Data Collection
Top of Page

Temporary Disk Space
(A) -- TNT: Refinement by Least Squares Function-minimization
TurboFrodo

Uppsala Software Factory: Gerard Kleywegt's Programs
UUDeview: A freindly uudecoder

VMD
vi Editor: A Unix based text editor
VNMR : NMR data acquisition, processing and display
VOLUME : Residue Voronoi Volumes
VRweb

Westhof Programs:RNA refinement and modeling package.
WHAT_IF
Wisconsin Sequence Analysis Package (GCG): The big one.

XALIGN: Multiple sequence alignment based on homology and secondary structure.
xdlDATAMAN and xdlMAPMAN
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
Xtalview
XV
XWPL and WPLIB: Wavelet Packets Analysis
XZAM

Top of Page

Last Modified: Friday, 13-Jan-2017 15:16:28 EST

RC Home | Search | Table of Contents | General Information

Richards Center (www.rc.yale.edu) at Yale University (www.yale.edu)
Contact: michael^strickler_at_yale^edu