Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00094 NAME CCP4 DOMAIN Crystallography DESCRIPTION The CCP4 Program Suite is an integrated set of DESCRIPTION programs for protein crystallography developed DESCRIPTION in a close collaboration between DESCRIPTION crystallographers under an initiative by the DESCRIPTION UK Science and Engineering Research Council. DESCRIPTION Some software developed elsewhere is included. DESCRIPTION Applications include data processing, various DESCRIPTION scaling programs, Patterson search and DESCRIPTION refinement, isomorphous and molecular DESCRIPTION replacement, structure refinement, phase DESCRIPTION improvement (solvent flattening and symmetry DESCRIPTION averaging) and presentation of results. AUTHOR - RT - ADDRESS SERC Daresbury Laboratory ADDRESS Secretary to CCP4, SERC Daresbury Laboratory, ADDRESS Warrington WA4 4AD, UK. CONTACT ccp4@daresbury.ac.uk. SITE ftp anonymous ccp4.dl.ac.uk (148.79.160.77) SITE Directory /pub/ccp4 SITE-CONTACT A.J.Bleasby@dl.ac.uk OS Sun Unix, Vax VMS LANGUAGE FORTRAN VOLUME - COMMENTS licence agreement is included with any COMMENTS distribution The suite is licensed free to COMMENTS academic institutions; the feeCS for profit- COMMENTS making organisations is currently 5000 pounds COMMENTS sterling. AC BC00095 NAME MOLSCRIPT DOMAIN Crystallography DESCRIPTION MolScript is a program for creating molecular graphics in DESCRIPTION the form of PostScript plot files. Possible representations DESCRIPTION are simple wire models,CPK spheres, ball-and-stick models, text DESCRIPTION labels and Jane Richardson-type schematic drawings of proteins, DESCRIPTION based on atomic coordinates in various formats. Colour,greyscale, DESCRIPTION shading and depth cueing can be applied to the various graphical DESCRIPTION objects. AUTHOR Per Kraulis RT - ADDRESS Pharmacia, Biopharmaceuticals R&D, N62:5 ADDRESS S-112 87 Stockholm, SWEDEN ADDRESS Tel: +46 (0)8 695 78 34 Fax: +46 (0)8 695 40 82 CONTACT per.kraulis@sto.pharmacia.se SITE WWW Server at URL http://www.avatar.se/molscript SITE WWW Server at URL http://www.avatar.se/molscript/obtain_info.html OS Silicon Graphics IRIS , the source code and makefiles will most OS probably work for other systems as well, such as ESV and IBM OS RS6000. For VAX/VMS, the i/o logical units in the source code OS will have to be changed. This you will have to do yourself LANGUAGE Fortran 77 VOLUME - AC BC00096 NAME XtalView DOMAIN Crystallography DESCRIPTION Complete packae for solving a macromolecular crystal structure DESCRIPTION by isomorphous replacement, including building the molecular model DESCRIPTION Free for non-profit users. Binary distribution is available through DESCRIPTION e-mail. source code is avalaible, but requires a signed license. AUTHOR Dr. Duncan E. McRee RA McRee D.E.; RT "A visual protein crystallographic software system for X11/XView."; RL J. Mol. Graph. 10:44-46(1992). RX SeqAnalRef; MCRD9201. ADDRESS The Scripps Research Institute, MB4 ADDRESS 10666 North Torrey Pines Rd., La Jolla, CA 92037, USA CONTACT dem@scripps.edu SITE WWW Server at URL http://www.sdsc.edu/1/Parts_Collabs/CCMS SITE-CONTACT ccms-help@sdsc.edu SITE WWW Server at URL http://www.sdsc.edu/0h/CCMS/Packages/xtalview OS Sun (Sun/OS and Solaris2.x) Dec/Ultrix, SGI LANGUAGE C, Fortran VOLUME - AC BC00396 NAME PERCH DOMAIN Crystallography DESCRIPTION PERCH (PEak reseaRCH) is an integrated software package offering DESCRIPTION some powerful tools for research on 1D-NMR spectra. DESCRIPTION PERCH takes advantage of 32-bit code, is running DESCRIPTION on IBM/compatible PC (386 or higher, math. coprocessor) and can DESCRIPTION be accessed from a graphical user interface under WINDOWS DESCRIPTION (picture) or command driven directly under DOS. AUTHOR PERCH Project RT - ADDRESS PERCH Project, University of Kuopio, P.O.B. 1627 ADDRESS FIN-70211 Kuopio, FINLAND ADDRESS tel: + 358 71 163242 - fax: + 358 71 163259 CONTACT perch@kummeli.uku.fi SITE ftp anonymous ftp.funet.fi SITE Directory /pub/sci/chem/nmr SITE-CONTACT - SITE WWW Server at URL http://www.uku.fi/~niemitz/perch.htm OS DOS LANGUAGE - VOLUME - REQUIRES - COMMENTS The 3 self extracting PERCH archives contain all COMMENTS necessary files and a setup program to ensure successful COMMENTS installation. MANUAL.EXE contains the manuals in WordPerfect 5.2 COMMENTS format. Extract the archives and follow the setup instructions COMMENTS in README.TXT. AC BC00400 NAME X-PLOR DOMAIN Crystallography DOMAIN Molecular modelling and graphics DESCRIPTION X-PLOR is a program system for computational structural DESCRIPTION biology. It is designed for exploration of the DESCRIPTION conformational space of macromolecules restrained to DESCRIPTION regions defined by both empirical energy functions and DESCRIPTION experimental data. The main use of X-PLOR is the refinement DESCRIPTION of structures determined by X-ray crystallography or DESCRIPTION nuclear magnetic resonance (NMR). X-PLOR offers the user a DESCRIPTION powerful high-level language for the manipulation of DESCRIPTION structural and experimental data. AUTHOR Axel Brunger's research group RT - ADDRESS For academic users : Chris Tambis, ADDRESS Dept. of Molecular Biophysics and Biochemistry, Yale University, ADDRESS P.O. Box 208114, 266 Whitney Avenue,Bass Center, ADDRESS New Haven, CT 06520-8114, USA. ADDRESS Commercial users should contact: ADDRESS Molecular Simulations, Inc., ADDRESS 16 New England Executive Park, ADDRESS Burlington, MA 01803-5297, USA. ADDRESS Phone: +1 - (617)-229-9800 ADDRESS Fax: +1 - (617)-229-9899 CONTACT ctambis@laplace.csb.yale.edu SITE ftp anonymous server.msi.com SITE Directory /pub/xplor SITE-CONTACT support@msi.com SITE WWW Server at URL http://xplor.csb.yale.edu/ OS Unix LANGUAGE - VOLUME - REQUIRES - COMMENTS The fee is $350, which covers the cost of media and COMMENTS postage, although if circumstances demand, this fee may be COMMENTS waived. A license must be completed before the code can be COMMENTS obtained. AC BC00433 NAME TURBO FRODO DOMAIN Crystallography DOMAIN Molecular modelling and graphics DESCRIPTION Turbo Frodo is a general purpose molecular modelling DESCRIPTION environnement aimed at people with the need to model de DESCRIPTION novo macromolecules, polypeptides as well as nucleic acids, DESCRIPTION to build such macromolecules from experimental 3-D data DESCRIPTION obtained from X-ray crystallography and NMr, to display the DESCRIPTION resulting models using various representations including DESCRIPTION Van der Waals and Connolly's molecular dot surfaces as well DESCRIPTION as spline surfaces. Compact views include CPK, icosahedra DESCRIPTION and ball -and- stick representations styles, alone or in DESCRIPTION combination. With Turbo Frodo, you can color your DESCRIPTION molecules according to different criteria, either DESCRIPTION objectively or subjectively, to compare them with existing DESCRIPTION structures and to evaluate their geometry. Turbo Frodo is DESCRIPTION also aimed at ligand fitting and protein stacking. You can DESCRIPTION interactively mutate a protein or chemically modify it, and DESCRIPTION evaluate the resulting conformational changes. Secondary DESCRIPTION structure calculation and their representation can be DESCRIPTION performed automatically. AUTHOR Alain Roussel PhD. headed by Christian Cambillau PhD. RA Roussel,A., and Cambillau, C.; RL Silicon Graphics Directory, Silicon Graphics Mountain View, CA,USA (1991) ADDRESS AFMB- Marseille France ADDRESS Tel: +33-91 11 77 98 - Fax: +33-91 61 25 67 CONTACT turbo@lccmb.cnrs-mrs.fr SITE - SITE-CONTACT - OS Sgi Unix LANGUAGE C VOLUME - REQUIRES Licence COMMENTS Turbo Frodo represents the new generation of graphics COMMENTS software because it has fast graphics and easy-to-learn COMMENTS pull down menus and dials. Plot files can be generated as COMMENTS Postcript files, which can be plotted on any postcript COMMENTS laser printer, such as for example the one of your COMMENTS Macintosh. COMMENTS Constant upgrading and maintenance ( 2 releases per year) COMMENTS are available. COMMENTS Turbo -X is a new extension of Turbo Frodo using X- motifs COMMENTS on Silicon Graphics Library , Hewlett Packard or on COMMENTS X-terminals ( Colour or black and white). It has most of COMMENTS the facilities found in the original program. COMMENTS For Nationals laboratories and academic research groups COMMENTS interim version of Turbo-X computer COMMENTS software is being made available as a B -site as is it developed. AC BC00553 NAME USF - Uppsala Software Factory DOMAIN Protein structure analysis DOMAIN Crystallography DESCRIPTION The Uppsala Software Factory provides software, DESCRIPTION web-based services and other resources for DESCRIPTION structural biologists (in particular, but not exclusively, DESCRIPTION for macromolecular crystallographers). DESCRIPTION All software can be downloaded free of charge by DESCRIPTION academics. For-profit insitutes and companies DESCRIPTION need to obtain a license. AUTHOR Gerard J Kleywegt AB http://alpha2.bmc.uu.se/~gerard/manuals/references.html AB http://alpha2.bmc.uu.se/~gerard/manuals/citing.html ADDRESS Dr. Gerard J. Kleywegt ADDRESS Department of Molecular Biology ADDRESS Uppsala University ADDRESS Biomedical Centre ADDRESS Box 590 ADDRESS SE-751 24 Uppsala ADDRESS SWEDEN CONTACT gerard@xray.bmc.uu.se SITE WWW Server at URL http://alpha2.bmc.uu.se/~gerard/manuals/ OS SGI, DEC Alpha OSF1, ESV LANGUAGE Fortran VOLUME varies REQUIRES varies .