Molbio software

George E. Applequist gea at IASTATE.EDU
Thu Aug 27 12:23:30 EST 1992


Here is something I received from Angela Loh at DEC (loh at mr4dec.enet.dec.com),
in case you are  interested in applications that run on RISC or VMS platforms.
You can contact a DEC representative for a DEC Science Applications Guide,
a 300+ page catalog with more detailed descriptions of the software you
see listed below.
                   
           KEY MOLECULAR SCIENCES APPLICATIONS ON DIGITAL PLATFORMS

                   DIGITAL EQUIPMENT CORPORATION
                      Science Marketing Group 
                       Revised June 16, 1992


COMPUTATIONAL CHEMISTRY:   

  AMBER (V*,VV*,R*)        Macromolecular Energy Refinement Program
  MM2, MM3 (V*,R*)         Allinger's Molecular Mechanics Programs
  MOPAC (V*,VV,R*)         Molecular Orbital Package
  GAMESS (V*,R*)           Ab Initio Electronic Structure Program
  MEPMAP (V*,R*)           Xwindow Display Program with GAMESS
  MOLPLT (V*,R*)           Xwindow Display Program with GAMESS
  PLTORB (V*,R*)           Xwindow Display Program with GAMESS
  DENDIF (V*,R*)           Xwindow Display Program with GAMESS
  GAUSSIAN80-UCSF(V*,R,VV) Ab Initio Electronic Structure Program
  GAUSSIAN92 (V*, VV*,R*)  Ab Initio Electronic Structure Program
  GROMOS (V*,R)            Groningen molecular Simulation Package
  FORTICON8 (V*,R*)        Extended Huckel Calculations
  BIGSTRN-3 (V*,R*)        General-Purpose Empirical Force Field Program
  LAOCN-5 (V*,R*)          Analysis of Isotropic NMR Spectra Systems
  ECEPP/2 (V*,R*)          Empirical Conformation Energy for Peptides
  CINMIN (V*,R*)           Mol. Geom. Optimization in CNDO/INDO Approx.
  LPT (V*,R*)              Linear Predictive Single-Value Decomposition of
                           Decaying Sinusoids for Spectral Analysis in NMR
  QCPE576 (V*,R*)          General Vibrational Analysis System
  COORD (V*,R*)            Atomic Cartesian Coordinates for Molecules
  AP (V*,R*)               General Fitting Program for Resolution of Complex
                           Profiles
  RNGCFM (V*,R*)           Exploration of Medium-Size Ring Conformation




V = VAX PLATFORMS
VV = VAX VECTORS
R = DEC RISC PLATFORMS 
* = AVAILABLE NOW
+ = PORTED, SUPPORT BASED ON CUSTOMER DEMAND
1 = AVAILABLE TO ACADEMIA ONLY
MPP = DECmpp PLATFORM


                                     




COMPUTATIONAL CHEMISTRY (continued):


  SPAMAT (V*,R*)           Solution of Linear Systems of Equations, 
                           Corresponding to Sparse Matrices
  1D/2D/3D (V*,R*)         Cubic Spline Interpolation Package
  STEPT (V*,R*)            Direct Search Optimization Solution of Least
                           Squares Problems
  ASYROTOR (V*,R*)         Asymmetric Rotor Energy Levels Program
  DIATH2 (V*,R*)           A Computer Aid for Studying the Quantum Mechanics
                           of the Chemical Bond
  CARCOR (V*,R*)           Cartesian Coordinates for All Atoms in a Molecule
  CEIG (V*,R*)             Eigenvalues and Eigenvector for (H-LS)C=O
  NESBET (V*,R*)           Eigenvalues and Eigenvectors for Large Matrices
  RACAH (V*,R*)            Racah Coefficients, 6J Symbols etc
  GIVENS (V*,R*)           Eigenvalues and Eigenvectors by the Givens Method
  NCRDWC (V*,R*)           Program to Determine Vibration Frequencies
  STOCHASTIC (V*,R*)       Stochastic Method for Finding All Molecular 
                           Conformations 
  CHARMM (V*,VV,R*)        Molecular Design and Dynamics
  CHEM-X (V*, R+)          Molecular Design Package Interfaces to Many Public
                           Domain Codes and its Specialized Modules
  DISCOVER (V*, VV*)       Molecular Simulation Package
  CONCORD (V*)             3D Molecular Structures Determination
  MACROMODEL's BATCHMIN    Dr. Still's Computational Code - to be used with
     (V*, R*)              FLIMMSY (X-11 Window System based interactive
                           graphical code) 


MOLECULAR MODELING:        

  DRAW-MOPAC (V*,R*)       MOPAC Molecular Drawing Program
  DENSITY (V*,R*)          MOPAC Electron Density Plotting Program
  Chem-Poly (V*, R+)       Polymer Modeling Module with Chem-X
  Chem-Movie (V*, R+)      High Performance Graphics Module with Chem-X
  Chem-Model (V*, R+)      3D Structural Analysis and Modeling
  Midas-Plus (V*,R*)       Molecular Modeling from UCSF
  BIOGRAF (V*, R*)         Molecular Simulation Package
  POLYGRAF (V*,R*)         Molecular Simulation for Polymer Research
  ENZYMIX (R)              Modeling of Enzymatic Reaction Mechanisms
  AVS CHEMISTRYVIEWER (R*) Molecular Graphics Software Used with DEC AVS
  YMOL (V*,R)              Molecular Stereoscopic Modeling 
  SYBYL (V*)               Molecular Simulation Package
  RING (V*,R*)             Closing a Cyclic Structure Exactly
  NAMOD (V*,R*)            Drawing Perspective Diagrams of Molecules
  DESSIN (V*,R*)           Drawings of Molecules on a Line Printer
  MFOLD (V*,R*)            Multiple RNA Folding and Secondary Structure 
                           Prediction
  FLIMMSY (R*)             Molecular Graphics Software for Macromodel
  WHAT IF (V*,R)           Molecular Modeling, NMR and X-Ray Package with
			    Graphics Program from EMBL
  FLEX (R*)		   Molecular Display Program from Scripps Clinic.
  SPARTAN (R*)		   Molecular Modeling Package from Wavefunction, Inc.





CRYSTALLOGRAPHY:

  XPLOR (V*,R*,1)          X-ray Crystallographic Refinement Program
  O (R*)                   X-ray Crystallographic Refinement Program
  TNT (V*,R*)              X-Ray Crystallography Refinement Modeling
  PROLSQ (V*, R*)          X-Ray Crystallography Refinement Modeling
  GSAS (V*,R)              General Structure Analysis System for Small 
                           Molecule Single Crystal and Powder
                           Diffraction Data
  PROTEIN (V*,R*)          X-ray Diffraction Analysis Software for Proteins
  XTAL 3.0 (V*)            Crystallographic Software System 
  Crystallography          MOTIF based Workbench for Crystallographers,
   Workbench (R*)          Developed at Columbia U, Distributed by ViSoft Inc.
  DF400-D (V*)             X-Ray Diffraction Application Software for Rigaku
                           X-Ray Diffraction Instruments
  SHELXTL PLUS (V*)        Structure Determination and Refinement for Siemens
                           X-Ray Instruments
  XENGEN (V*,R)            Protein Area Detector Data Processing Software
  MADNES (V*, R*)          X-Ray Diffraction Collection System for Electronic
                           2-Dimensional Position Sensitive Detectors
  XMONITOR (R*)            Real Time Graphical Monitoring and Evaluation of
                           Protein and Virus Crystallography Data
  XMAPEDIT (R*)            Graphical Package for Molecular Envelope 
                           Determination 
  XDISPLAYF (R*)           2-D Diffraction Analysis Package
  XELOP (R*)               3-D Diffraction Analysis Package
  XtalView (R*)		   X-11 Based Visual Protein Crystallographic 
			   Software System 
  Platon (V*)              A Single Crystal Structure Determination Tool from
			   U of Utrecht
  CCP4 (V*,R*)             A Suite of Programs for Protein Crystallography
			   distributed from Daresbury Laboratory
  Molscript (R*)	   Molecular Schematics Drawing Program
  XDS (V*,R*)		   Area Detector Data Processing Software
  OSCDEC (R*)	           MGR Film Processing Program
  GLRF (V*, R*)            General Locked Rotational Function
  TF (V*,R*)		   Translational Function
  PATSOL (R*)		   Patterson Interpretation Program
  HKLAVG (R*)		   Reciprocal Space Averaging Program


NUCLEAR MAGNETIC RESONANCE (NMR):

  NMR-GRAF (V*,R*)         Molecular Structure Determination and Simulation   
                           from NMR Data
  NMR-1, NMR-2 (V*,R*)     NMR Analysis Software
  NMR-Z (V*, R*)	   NMR Analysis Software
  NMR-Model (V*,R*)        Molecular Modeling with NMR Data
  ANSIG (R)                Assignment of NMR Spectra by Interactive Graphics
  FELIX (R*)               NMR Data Processing Software
  DSPACE (R*)              Graphical Program for Structure Determination
                           from NMR Data          
  Bruknet (R*)             Interface to Bruker NMR Instruments
  CSearch (V*)		   NMR Spectrum Prediction Program 





GENETIC ENGINEERING:       

  WISCONSIN PACKAGE (V*,R) Comprehensive Genetic Sequencing Tools
  BLAZE (MPP*)             High Sensitivity Sequence Similarity Search Program
  EUGENE/SAM (R*)          Genetic Sequencing Tools
  MAPMAKER-II,-QTL (V*,R*) Genetic Mapping Tools
  MBCRR SET (R*)           DNA and Protein Sequencing and Structure Analysis
  PROPHET (V*,R*)          Bioresearch Tools
  IntelliGenetics Suite(V*)Genetics Sequencing Tools
  CAGE/GEM (V*)         



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