Redasoft Plasmid 1.1: software for easy, efficient cloning and map drawing

A computer program is described which creates circular and linear genetic maps with or without sequences, performs restriction analysis, and simulates basic molecular cloning operations. Redasoft Plasmid 1.1 is a user-friendly program for Windows 95/98/NT/2000, designed to generate high quality genetic maps for presentation and publication and to aid the molecular biologist in selecting restriction endonucleases for common molecular cloning experiments. The program incorporates an integrated web browser and can automatically generate complete, labeled maps from sequences on the Internet.     

A computer program for processing data from amino acid analysis and for the calculation of molecular weights from those data.

A computer program is described for the calculation of the complete amino acid composition of a protein from the analytical data. The program also derives a molecular weight on the basis of the amino acid composition. The use of the program for the determination of the molecular weights of the liver carboxylesterases of chicken, horse, ox, and sheep is described.     

VESICA: Computer graphics modeling of lipid vesicles

A vesicle simulation and computer analysis program, VESICA, is described which employs spherical projections of triangularly tessellated icosahedra to produce molecular graphics models of the three-dimensional structures of lipid vesicles. The program is used to analyze the molecular architecture of small unilamellar vesicles of dipalmitoylphosphatidylcholine and is demonstrated as a worthwhile investigative tool for determining the factors that govern the minimum vesicle size.     

WinMGM: A fast CPK molecular graphics program for analyzing molecular structure

A molecular modeling program is presented which has been written for Microsoft windows 3.1 and Windows NT operating systems. The program permits interactive molecular manipulation and also provides analytical tools such as energy computations and solvent accessible surfaces. An extremely fast algorithm is used which generates realistic space-filling CPK images in addition to wire frame, ribbons, MIDAS, labels, and points. An important feature of this algorithm is a highly optimized Z-buffer, which is described.     

Calculation and display of electrostatic potentials

A general methodology is developed for incorporating accurate electrostatic information from ab initio molecular orbital calculations into molecular mechanics calculations. Examples are given of the method applied to simple aromatic organic molecules. A program has been developed for displaying the results of the ab initio calculations on a Silicon Graphics workstation. The technique developed here provides an alternative method for including electrostatic interactions in molecular mechanics calculations and is compared with other methods for determining atomic charges.     

Tek FRODO: A new version of FRODO for Tektronix graphics stations

A new version of the molecular graphics program FRODO was developed to allow the range of Tektronix graphics stations to be used for molecular modeling and crystallographic applications. The work was divided into two parts: first, the universal molecular modeling graphic package (Tek_MMGP) was written to enable basic modeling operations for Tektronix stations. Second, all routines of FRODO involving computer graphics were modified to fit the new hardware environment, and linked with Tek_MMGP. The resulting package, Tek_FRODO, has been used successfully for crystallographic refinement in several projects. The program, written in FORTRAN, is ready to be ported to any of Tektronix 3D graphics stations; it is available from the authors on request.     

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.     

A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.     

Computer prediction of peptide maps: assignment of polypeptides to human and mouse mitochondrial DNA genes by analysis of two-dimensional-proteolytic digest gels.

We have prepared a computer program that predicts complete and partial peptide maps from amino acid sequences. The program fragments amino acid sequences at designated cleavage sites and calculates the molecular weight and relative labeling of each peptide. These data are graphed as log molecular weight of the original protein (X-axis) vs. log molecular weight of the component peptides (Y-axis). The program is interactive, permitting adjustment of a number of graphic parameters and alteration of the position of proteins in the first dimension to accommodate aberrations in protein mobility. The program has been used to predict the V8 protease peptide maps of the 13 open reading frames (ORFs) identified in the human and the mouse mitochondrial DNA (mtDNA) sequences. The results were compared to the V8 protease peptide maps obtained for mouse and human mitochondrially synthesized proteins by two-dimensional proteolytic digest gels. A high correlation was observed between the predicted and observed peptide maps. These results suggest the assignment of several proteins to mtDNA genes.     

Ab initio Molecular Electrostatic Potential Grid Maps for Quantitative Similarity Calculations of Organic Compounds

The program MolSim designed to calculate the similarity of different molecules quantitatively in a fast and easy way is described. The molecular similarity is estimated for the molecular shape as well as for the electrostatic potentials of the molecules derived from ab initio calculations. A grid-based method is used to determine the steric and electrostatic similarities between a lead compound and the corresponding test set by calculating the Spearman correlation coefficient. The superpositioning of the molecules was accomplished with the SEAL algorithm incorporating a Monte Carlo simulated annealing approach while preserving the conformational flexibility of the calculated structures.The ability of the program was tested on a set of Sandalwood odour compounds, a class of substances that is difficult to analyse with respect to its structure-activity relationship because of the structural diversity of Sandalwood odour compounds, in contrast to their high selectivity and pronounced structural specificity. The application of the program on a small test set of these compounds showed that the program is able to explain the Sandalwood odour activity correctly.Electronic Supplementary Material available.     

VisiCoor: A simple program for visualization of proteins

A well-drawn picture acts as an excellent metaphor for something real, and human vision provides instant, random access to any part of which the picture represents. It is in this sense that pictures can convey information more effectively than words alone. The power of the graphics work-stations available today makes visual presentation of scientific results a reality. A molecular graphics program for investigating protein structures, as well as several sample plots that show the power of the program, are presented.     

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.     

Theoretical studies of the electrostatic potential of some enzyme inhibitors using computer graphics techniques

A molecular graphics program is described for the depiction of electrostatic potentials on the van der Waals surface of molecules, using colored polygons. An example is given on the application of this method to the study of coumarins and flavones that inhibit the enzyme Glyoxalase I.     

Supramol--a program for structure analysis of intercalates using molecular simulations: the structure of VOPO4*C6H4O2

A method of structure analysis of intercalates has been developed that uses a combination of molecular simulations with powder diffraction. The program Supramol for the determination of intercalated structures uses crystal energy minimization in conjunction with powder diffraction data.The program solves the multiple minima problem in molecular mechanics, generating initial models systematically and searching for the global energy minimum by comparing the experimental and calculated diffraction patterns. The program is compatible with the Cerius2 modeling environment.Two intercalated crystal structures solved by Supramol are presented in the present paper: vanadyl phosphate intercalated with p-benzoquinone and the high temperature phase of vanadyl phosphate intercalated with dioxane. The structure of vanadyl phosphate intercalated with p-benzochinone is tetragonal, space group I4/ m, the unit cell parameters a=6.21 A, b=6.21 A, c=20.18 A and the density is rho=2.30 g x cm(-3), Z=4. The crystal structure of vanadyl phosphate intercalated with dioxane (high temperature phase) is monoclinic, space group C2/ m, unit cell parameters are: a= b=8.94 A, c=8.22 A, alpha=gamma=90 degrees, beta=106.30 degrees, Z=4, density 2.248 g x cm(-3).     

Molecular Dynamics Simulations of Proteins in Water Without the Truncation of Long-range Coulomb Interactions

A new program package (COSMOS90) for molecular dynamics simulations was developed to simulate large molecular systems consisting of more than tens of thousands of atoms without the truncation of long-range coulomb interactions. This program package was based on a new approximation scheme (PPPC) for calculating efficiently the coulomb interactions without sacrificing accuracy. In this approximation scheme, the group of charges at a long distance from each atom was represented by a total charge and total dipole moment of the group. In order to assess the accuracy of PPPC and the ability of COSMOS90, molecular dynamics simulations were carried out for a large system consisting of 16108 atoms (human lysozyme in water) for 50 ps using this program package. The coulomb energy per solute atom was calculated with only five percent of the error found in the 10 Å cut-off approximation (about 0.9 kcal/mol versus 18 kcal/mol, respectively). The molecular dynamics simulations using COSMOS90 require no more CPU time than the simulations based on the 10 Å cut-off approximation of the conventional programs for macromolecular simulations.     

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.     

Robust estimation of standard curves for protein molecular weight and linear-duplex DNA base-pair number after gel electrophoresis

An accurate procedure for estimating linear-duplex DNA base-pair numbers and protein molecular weights after electrophoresis in single concentration gels is presented. A robust modified hyperbola was found to be superior for determining molecular weights and base-pair numbers for a set of known standards when compared with the conventional log transformation and a similar hyperbolic model. We describe the use of a soft laser-scanning densitometer to measure band-migration distances of wet, stained polyacrylamide gels for proteins and photographic negatives of agarose gels containing DNA stained with ethidium bromide. This automated densitometric method was more accurate than existing methods. A BASIC computer program detailing the procedure is included.     

CX,an algorithm that identifies protruding atoms in proteins

MOTIVATION: A simple and fast algorithm is described that calculates a measure of protrusion (cx) for atoms in protein structures, directly useable with the common molecular graphics programs. RESULTS: A sphere of predetermined radius is centered around each non-hydrogen atom, and the volume occupied by the protein and the free volume within the sphere (internal and external volumes, respectively) are calculated. Atoms in protruding regions have a high ratio (cx) between the external and the internal volume. The program reads a PDB file, and writes the output in the same format, with cx values in the B factor field. Output structure files can be directly displayed with standard molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB Viewer and colored according to cx values. We show the potential use of this program in the analysis of two protein-protein complexes and in the prediction of limited proteolysis sites in native proteins. AVAILABILITY: The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/CX or on request from the authors.