From: gea@IASTATE.EDU (George E. Applequist)
Subject: Re: Molbio software
Reply-To: gea@IASTATE.EDU (George E. Applequist)
Organization: Iowa State University
Date: Thu, 27 Aug 1992 17:23:30 GMT

Here is something I received from Angela Loh at DEC (loh@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*)            Genetic Engineering Toolkit
  REPLICA (V*)             Multiplex DNA Sequence Reading, Access to Film Image
  Kepler 1-D/2-D Gel       Gel Processing and Analysis and Database 
   Analysis  System (V*)    Management
  Staden (R*)		   Automated Sequence Input, Editing and Analysis
  Tulla (V*)		   Multiple Protein/DNA Sequence Alignment
  Genetic Data Environment Workbench, Integrated Tools for DNA and Protein 
   (R*)			   Sequence Analysis
  GTAC (V*)		   Automatic DNA Sequence Assembly
  MASE (R*)		   Multi Alignment Sequence Editor
  NCBI Software            Tools to Access ASN.1 Dta, String Comparisons, from
   Development Kit (V*,R*) NCBI/Genbank
  PIMA.SH (R*)		   Pattern Induced Multi-Alignment Algorithm for Amino
			    Acid Sequencing
  PLSEARCH (R*)		   Protein Homologous Family Pattern Library and 
			    Search Tool
  S.A.G.E. (V*, R*)	   Statistical Analysis for Genetic Epidemiology
  GRAIL (R*)		   AI System for Gene Recognition and Interpretation
  EMBL Suite (V*, R)	   Tools for Genetic Sequencing
  Integrated Genome DB &   NIH/DCRT Mapping & Sequencing Database and Graphics
   Genographics (R)	    Interface			   

ELECTRON MICROSCOPY (EM):

  MDPP/NYU (V*,R*)         Electron Microscopy Image Processing and Analysis
  I-MAGIC 5 (R*)           Electron Microscopy Image Processing and Analysis
  EM (V*)                  U Chicago Electron Microscopy Image Processing and
                           Analysis 
  ANALYZE/Mayo Clinic      Multidimensional Biomedical Image Display & 
   EM (V*)		    Analysis
  Distributed Imaging/     Visualization & Multimodality Biomed Image
   Wash U. (MPP)	    Reconstruction




DATA ACQUISITION, ANALYSIS AND MANAGEMENT:

  ABI 373 Programming	   Library of Routines for Data Extraction from Files 
   Toolkit (R*)		    Created by the ABI 373A DNA Sequencer
  Digital Realtime Test    Toolkit to Facilitate Instrument Connectivity and
   Integrator (V*,R*)       Data Acquisition and Analysis       
  CAMAC (V*)               Realtime Data Acquisition I/O Subsystems
  INSTINCT (V*) 	   DECrti Based Control/Set Up Package for CAMAC
  WATERS CHROM (V*)        Realtime Data Acquisition of Chromatography Data
  Expert Ease (V*)	   Waters Chromatography Data System
  Fisons Chromatography Server
   (V*, R*)                Realtime Data Acquisition of Chromatography Data
  Multichrom 2 (V*)        Fisons GC and HPLC Data System
  XChrom (V*, R*)	   Fisons GC and HPLC System under X Window System
  ACCESS*CHROM (V*)	   Multiuser, Multitasking Chromatography Data System
  PeakPro Chromatography
   Data System (V*)        Beckman's System for GC, HPLC and IC
  ICIS-II (R*)             Mass Spectrometry Data Acquisition and Analysis
  Fisons LIMS (V*)	   Laboratory Information Management System
  Lab Manager LIMS (V*)    Beckman's Laboratory Information Management System 
  SQL*LIMS (V*)	   	   PE Nelson's Laboratory Information Management
			   System
  Alert (V*)		   Package for Product Safety Data Collection, 
 			    Assessment, and Reporting
  Alert/CURRENT CONTENTS   Software to Develop and Maintain Institute for
   Search System (V*)	    Scientific Information (ISI) Database
  FACS/DESK (V*)	   Data Collection, Analysis, and Management Package
			    for Fluorescence-Activated Cell Sorter Instruments
  RS/Discover (V*)	   Data Analysis tool for Design of Experiments
  RS/QCA II (V*)	   Tool for Statistical Quality Control
  SpectIR (V*, R*)	   Tool for Infrared Data Processing


STATISTICAL ANALYSIS AND MATHEMATICAL TOOLS:      

  The SAS System (V*,R*,VV)Data Analysis and Display
  SPSS-X, SPSS Graphics 
   (V*,R*)                 Data Analysis and Display
  RS SERIES (V*,R)         Data Analysis and Display
  IMSL LIBRARIES (V*,R*)   Libraries of FORTRAN Subroutines   
  NAG FORTRAN Library 
   (V*,R*)                 Libraries of FORTRAN Subroutines
  BCSLIB (V*)              Mathematical Subprograms
  Mathematica (R*)         System for Mathematical Computation
  BLSS (R*)                Statistical Analysis from U. Calif. at Berkeley
  Maple (V*,R*)            Symbolic Mathematics Software from Waterloo Maple
                            Software Co. 
  Stata (R*)               Statistical, Graphics and Data Management Software


  

VISUALIZATION TOOLS:

  DEC AVS (R*)             Application Visualization System Environment
  DI-3000 (V*,R*)          2D and 3D Graphics Software Tools Package
  apE (R*)                 Visualization Toolkit for Imaging, Volume and 3D
                           Graphics
  NCSA X-Image (R*)        Tool for Displaying Slices, and Isosurfaces
  NCSA X-DataScope (R*)    Tool for Volumetric Rendering
  GRAFkit (V*,R*)          Graphics Package for Multi-dimensional Data
  MOVIE.BYU (V*,R*)        Data Display and Manipulation
  Paragon-IPS (V*,R*)      Image Processing Software
  PV-WAVE (V*,R*)          Graphics Data and Analysis Software
  Visualization Workbench  A Visual Programming Language Integrating Image
   (R*)                    Processing and Graphics
  The Advanced Visualizer,
   The Data Visualizer, &
   The Personal Visualizer
   (R*)                    Imaging, Animation and Simulation System 
  GIPSY (V*,R*)            General Image Processing System
  ANALYZE Software (R*)    Tools for multidimensional image data analysis
  MRI/Image (V*, R*)       Magnetic Resonance Imaging Analysis and Processing

  
OTHER MODELING:      
  
  Genesis and Xodus (R*)   Neurobiology Network Modeling
  Saber (R*)               Neurology Simulation Software
  SAAM II (V*,R*)          Simulation, Analysis and Modeling Tool 
  PHOENICS (V*,VV,R)       Fluid Dynamics Software
  FLUENT, FLUENT/BFC
   (V*,VV,R*)              Fluid Dynamics Software
  FIDAP (V*,VV,R*)         Fluid Dynamics Software
  ARC-2D (V*,VV*,R)        Finite Difference Software
  DYNA 2-D, DYNA 3-D 
   (V*,VV,R)               Finite Element Analysis
  KIVA2 (V*,VV,R)          2D, 3D Chemical Reactive Fluid Flow with Sprays 
  TACO3D (V*,VV, R)        Heat Transfer Analysis, 3D Finite Element Analysis 
  TOPAZ3D (V*, VV, R)      Heat Transfer Analysis, Finite Element Analysis
  TAURUS (V*, VV)          Plotting Application Interfacing with DYNA3D,
                           TACO3D, TOPAZ3D, etc.                        




CHEMISTRY DATABASES:       
 
  CAS ONLINE (V*)          Chemical Abstracts Services' Databases
  NBRF Protein (V*)        Protein Sequence Library
  NBRF Nucleic (V*)        Nucleic Acid Sequence Library
  EMBL (V*)                Nucleic Acid Sequence Library
  GENBANK (V*)             Nucleic Acid Sequence Data Library
  Swiss-Prot (V*)          University of Geneva Protein Sequence Library
  VecBase (V*)             Database of Vectors
  REACCS (V*)              Compound and Reaction Database Package
  MACCS-3D, MACCS-II (V*)  2D and 3D Chemical Structure Databases Package    
  ISIS (V*)                Structures and Related Database System  
  ChemDBS-3D (V*,R+)       3D Structures Database Includes Chapman & Hall
                           Chemical Dictionaries
  Grateful Med (R*)        Library search interface to Medline
  Daylight Toolkit (V*,R+) Chemical Information Handling and Modeling Software


SOFTWARE DEVELOPMENT OR C.A.S.E.:

  VAX FORTRAN (V*,VV*)     Fortran for Ultrix and VMS Systems
  DEC FORTRAN (R*)         Fortran for RISC based Systems
  VAX C (V*,VV*)           C Compiler for Ultrix and VMS Systems 
  GNU C++ (R*)             C++ Compiler 
  Saber C (V*,R*)          C Compiler
  C TOOLS (R*)             File/Code Manager Tools
  UNIX CASE Tools (R*)     Common Tools Available with UNIX
  Prolog (V*,R*)           Prolog Compiler
  LISP (V*,R*)             LISP Compiler
  TeX, VorTex, LaTeX(V*,R*)Text editors
  VAXset (V*, VV*)         Set of software development tools   
  Many others are available