CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO

We have implemented in TOM/FRODO a protein crystallographic symmetry display and handling package, called CRYStallize. This package is designed as an aid in solving protein structures by molecular replacement methods. It allows the rotation/translation solutions provided by molecular replacement programs to be checked in a fast and easy way. Using CRYStallize, approximate solutions can also be improved by manual modifications. Symmetry-related objects, represented as surfaces, can be generated and handled in the same way as the reference molecules, thus permitting an efficient analysis of crystal packing and site accessibility. This program is available in the TOM/FRODO software release, which runs on the Silicon-Graphics workstations.     

Molecular conformational space analysis using computer graphics: Going beyond FRODO

The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed.     

Comparison of computer modelling and X-ray results of the binding of a pyrazole derivative to liver alcohol dehydrogenase

The binding to liver alcohol dehydrogenase of the inhibitor 2,4-(4-pyrazolyl)-butylisothiourea has been studied both by modelling experiments using computer graphics with interactive energy minimization and by X-ray crystallographic structure determination. For the modelling experiments, we used the program system TOM, which was developed in our laboratory as an extension of the program FRODO. Different strategies for using computer graphics with interactive energy minimization were tested. Two essentially different binding modes were found. One of these was favoured from energy minimizations using a potential energy function which was the sum of a Coulomb interaction term and two different van der Waals' interaction terms for non-bonded and torsional interactions. This binding mode was close to the crystallographic observed structure. The results show that flexibility of both ligand and receptor side-chains as well as main-chain conformations are important for docking to the active site of liver alcohol dehydrogenase.     

PUCK: a real-time modification of sugar pucker on a PS300

This paper describes a program for a real-time interactive modification of furanose sugar pucker. The resulting change of conformation is visualized instantaneously on the display screen of an Evans and Sutherland PS300, the picture system on which the program was implemented. The program is accessible as a new function, named PUCK, in the molecular modeling system FRODO. This new possibility fills the lack of degrees of freedom for modeling nucleic acids.     

A program for reading DNA sequence gels using a small computer equipped with a graphics tablet.

A program has been written in BASIC that allows DNA sequence gels to be read by a Tektronix model 4052 computer equipped with a graphics tablet. Sequences from each gel are stored on tape for later transfer to a larger computer where they are melded into a complete overall sequence. The program should be adaptable to other small computers.     

Use of techniques derived from graph theory to compare secondary structure motifs in proteins

A substructure matching algorithm is described that can be used for the automatic identification of secondary structural motifs in three-dimensional protein structures from the Protein Data Bank. The proteins and motifs are stored for searching as labelled graphs, with the nodes of a graph corresponding to linear representations of helices and strands and the edges to the inter-line angles and distances. A modification of Ullman's subgraph isomorphism algorithm is described that can be used to search these graph representations. Tests with patterns from the protein structure literature demonstrate both the efficiency and the effectiveness of the search procedure, which has been implemented in FORTRAN 77 on a MicroVAX-II system, coupled to the molecular fitting program FRODO on an Evans and Sutherland PS300 graphics system.     

A crystallographic molecular lattice builder applied to model lipid bilayers

It is often desirable for noncrystallographers to generate graphical models of three-dimensional crystal structures based on published coordinates of the atoms that make up the crystallographic unit cells. This type of visualization is particularly important for small-molecule crystals, such as lipid crystals, where one may be interested in investigating interactions between the individual molecules in addition to their conformations. BILAYER BUILDER is a program that generates a portion of the entire crystal structure from the coordinates of the molecules in a single unit cell. It gives users of small desktop computers, such as the Apple Macintosh, the capability to generate and examine model crystal structures with a molecular graphics display program. BILAYER BUILDER stores the crystal coordinates in a Brookhaven Protein Data Bank file format for possible use in a variety of applications on many different computers. Initially, it was written for use with lipid crystals and bilayers but may be used for building an assortment of molecular crystals.     

New programs: XELE—a polypeptide model-building program for a graphics workstation

A model-building program, XELE, for use in protein crystallography has been written in C under UNIX on a graphics workstation. This program makes full use of the X Window system to display the electron density distribution and to manipulate the polypeptide model, and therefore is named XELE. It utilizes a fast three-dimensional rendering package, Dorè, and is portable to other types of graphics workstations. A part of the program for the man-machine interface uses the library of X Window and X Toolkit, and therefore is highly interactive. The structure analysis program package, PROTEIN, is also implemented in an interactive mode using X Window, and has been interfaced with XELE.     

BRAGI: A comprehensive protein modeling program system

A protein modeling program package has been developed. The user friendly system is implemented on high performance graphic devices and facilitates the modeling of a protein with an unknown three-dimensional structure out of that of a homologous one or the design of new variants. A wide range of features can be used by the researcher for this purpose. The system is written in FORTRAN 77 and E&S GSR functions or the HP implementation of the PHIGS standard, respectively.     

MoG: Molecular graphics software for the Commodore Amiga

As recently described by Garavelli, the Commodore Amiga 3000 computer is “nearly ideal” for desktop molecular modeling. The chief drawback to date, has been the lack of suitable software. This paper describes a new desktop molecular modeling package, MoG, which is suitable for both research and educational use. The speed of the Amiga 3000 means that MoG competes very favorably with software on IBM-PC machines, and its graphics capabilities allow excellent space-filling representations. The availability of cheap software-compatible home-computer versions of the Amiga places interactive molecular graphics within the reach of many senior high-school students, undergraduates and graduate students.     

MOLPACK: molecular graphics,for studying the packing of protein molecules in the crystallographic unit cell

A graphics program, MOLPACK, has been developed on the Silicon Graphics IRIS-4D computer system for displaying the packing of proteins in the crystallographic unit cell. In addition to the normal viewing operations of rotation, translation and scaling, the program has the ability to translate molecules along the cell axes while maintaining their crystallographic equivalent positions within the unit cell. This allows the user to observe the packing of protein molecules generated by molecular replacement, to create a new packing model or to locate an unknown molecule. A special feature of the program is that up to four independent molecules can be manipulated in the asymmetric unit.     

APE: Analyses of Phylogenetics and Evolution in R language

Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.     

Interactive program for visualization and modelling of proteins,nucleic acids and small molecules

The graphics package Insight for the DEC VAX and Evans and Sutherland PS300, created as part of a joint university-industry research project, provides a broad set of capabilities which allow the user to display molecular models in stick figure and surface representation. The Insight program allows the user to model and manipulate proteins, nucleic acids and small molecules. The software accepts coordinate input from several possible sources and provides both a command and menu interface for manipulation of the graphics objects. The command language and program structure make it easy for the biochemist or molecular biologist to use.     

Adopting a database as a solution to managing electron image data

A database was used for data management and interprogram communication in an image processing and three-dimensional reconstruction program suite for biological bundles. The programs were modified from the MRC crystallographic package. The database server works with local and remote programs and data sets, allows simultaneous requests from multiple clients, and maintains multiple databases and data tables within them. It has built-in security for the data access. Several graphical user interfaces are available to view and/or edit data tables. In addition, FORTRAN interface and function libraries are written to communicate with image processing software. The data management overhead is inexpensive, requiring only narrow bandwidth from the network. It easily handles several data tables with over 1000 entries.     

ProteinShader: illustrative rendering of macromolecules

Background

Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings.

Results

The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline.

Conclusion

By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images.     

PCDRA: PC interactive molecular representation and modeling system

PCDRA was designed to provide the average biologist with a user-friendly molecular display on a low-cost personal computer. The package is menu driven and is built so that a biologist, with tittle or no computing knowledge, finds it easy to use. The system gives a color representation with depth cueing of a protein whose atomic coordinates are stored as a PDB file. Moreover, the system presents several features similar to HYDRA¹ and therefore is a good introduction to molecular graphics, especially for beginners in protein modeling.     

AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages

A program for converting the different existing AMBER and GLYCAM force fields for use with commercial molecular modeling packages is presented, using the Molecular Simulations Inc. (MSI or Accelrys) software package as a case model. Called AmberFFC, the program creates AMBER and GLYCAM force field files suitable for use with the Accelrys molecular mechanics modules by transforming the amino acid, nucleotide, and monosaccharide topology databases and force field parameter files to the Accelrys file format. It is intended for any modeler who is interested in using the current AMBER and GLYCAM force fields with the Accelrys FDiscover and CDiscover programs. AmberFFC has been written entirely with the Perl programming language, making it highly flexible and portable. In order to compare the implementation of the force fields converted by AmberFFC in the Accelrys package with their corresponding execution in the AMBER software, and also to verify the efficiency of the AmberFFC program, results from single point energy calculations for 13 model molecules were obtained with the two programs. It is demonstrated that results obtained with the CDiscover and FDiscover modules compare well to those found using Sander_classic, thus showing that AmberFFC is a highly efficient program. Some energy differences between the AMBER and Accelrys software have been observed, and their origin has been characterized and discussed.     

PEPCRE: an interactive program to create,manipulate and display oligopeptides

PEPCRE is an interactive computer graphics program for the rapid construction, manipulation and display of oligopeptides. Essentially any desired conformation of an oligopeptide can be constructed in a simple and straightforward manner. The program provides various display and output possibilities. It is user-friendly and is written in FORTRAN 77 for use on inexpensive, monochrome graphics terminals.