HCABAND: A computer program for the 2D-helical representation of protein sequences

A BASIC program, HCABAND, is described which is used to convertthe linear amino acid sequence of proteins into a word processor-readablefile to generate the 2D-helical representation required forhydrophobic cluster analysis. The user can specify the widthof the plot and can use the word processor macro-commands tofacilitate visual inspection of the plots. The plots can beeasily stored on diskettes, mixed with text and printed. HCABANDfeatures are generally applicable and can be implemented onvirtually any microcomputer. Received on May 9, 1989; accepted on August 28, 1989     

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.     

Three-dimensional structure model for benzenoid musks expressed by computer graphics

Structures of two strong benzenoid musks, 3,5-di-t-butylacetophenoneand 5-acetyl-1,1,2,3,3,6-hexamethylindan, were optimized byPM3 (MOPAC Ver.5). Based on these structures, a three-dimensionalstructure model for benzenoid musks was constructed. This structuremodel is expressed as a box of about 12 x 11 x 6.5 Å Whichcircumscribes musk molecules. The box contains (i) a smallerbox of about 7.5 x 11 x 6.5 Å Which approximates the hydrophobicbulky moiety of benzenoid musks; (ii) the position of the benzenering located in the smaller box; and (iii) the binding pointon an odor receptor assumed to interact with an oxygen atomof the functional group in the benzenoid musks. The validity of this structure model was examined by applyingit to structures of 40 benzenoids (30 musks and 10 odorless).As a result, 37 out of the 40 benzenoids were correctly discriminatedto be odoriferous or odorless by referring them to this structuremodel.     

Three-dimensional structure of protein C inhibitor predicted from structure of alpha 1-antitrypsin with computer graphics

The three-dimensional structure of a proteolytically modified protein C inhibitor, a member of the serine protease inhibitor superfamily, was constructed with computer graphics based on its amino acid sequence homology with that of the modified alpha 1-antitrypsin whose structure had been elucidated by X-ray crystallography. The intact form of protein C inhibitor was predicted with an alpha-carbon model based on its hydrophilicity and hydrogen bond pattern. Furthermore, a model of its interaction with activated protein C was constructed based on the structure of the complex between trypsin and its inhibitor, which had been determined by X-ray crystallography.     

A novel representation of protein structure

Using a nonlinear mapping technique, we demonstrate that proteins folded in two dimensions display the same overall structural features as their three-dimensional counterparts. The two-dimensional representation of protein structure provides a novel way to visualize structural as well as distance information. It may also provide a link for deriving three-dimensional structure from amino acid sequence.     

A one-dimensional representation of protein structure

A one-dimensional representation of protein structure in terms of angles between C_αC_α links in a two-dimensional representation describes tertiary structure to an accuracy of approximately 3 Å.     

A computer program for characterizing root system branching patterns

A computer program is presented which measures the length, branching patterns and distribution of link length within a root system. The program skeletonizes digitized images of root systems, loads these images into a binary tree data structure and uses this data structure to characterize the root systems. Measurements of the root length and topological parameters of root systems of Senecio vulgaris made by hand and by computer program were linearly related, with r² values greater than 0.99 in all cases.     

MANOSK: A graphics program for analyzing and modeling molecular structure and functions

A program written for the Evans and Sutherland PS300 graphic displays is described in this paper. Called MANOSK, it provides a flexible and powerful environment for displaying, manipulating and analyzing small molecules and macromolecules from atomic coordinates. Translations and rotations of up to four independent molecules are available from the dials, and screen-relative orientations of the molecules are used in all geometrical and energetical calculations. A gradual progression of functions complexity makes the program easy to use for occasional works and efficient for more sophisticated studies.     

A computer program for translating DNA sequences into protein.

This paper describes a comprehensive program for translating one or two DNA sequences into amino acid sequences. Written in FORTRAN, it was designed for maximum flexibility of use and easy maintenance, modification and portability. It has full comments throughout.     

A fast graphics printing program for neurophysiological data

A program was written in assembly language for fast graphicsscreen dump of neurophysiological data during and after experiments.This program takes 3 s to plot a 1024 x 768 graphics image.A resident program has also been produced, which allows a screengraphics image to be printed by using a keyboard command. APascal-compatible object file is available to interface theprogram with Turbo-Pascal programs.     

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.     

Comparison of protein structural profiles by interactive computer graphics

This paper describes a novel computer graphics tool for predicting protein structures. The method is based on structural profiles; which are plots of hydrophobicity, parameters used for secondary structure prediction, or other residue-specific traits against sequence number. Similar structural profiles can indicate similar tertiary structures, in the absence of sequence homology. The profiles of reference proteins, with known structure, can be used for prediction. In the method presented here, structural profiles are compared by interactive computer graphics, using the program Multiplot. As a test, a structural profile comparison of several proteins known to have similar 3D structures is presented. Comparison of structural profiles detects similar folding of the two domains of rhodanese, which was not easily detected by sequence homology.     

Fragment library-based representation system for protein conformation

The representation system for protein conformation has a crucial effect on the speed of various protein-related simulations, including ab initio protein structure prediction and protein-protein docking simulation. Usually, the finer a representation system, the longer is the computational time required to employ the representation system in simulations. On the other hand, very coarse lattice systems cannot be directly applied to the simulation problems with real proteins. We report a new, fragment library-based protein conformation representation system, prepared by clustering amino acid conformations from 154 proteins. This system was composed of 64 most representative fragments per each amino acid, and based on the unified residue approach in which two spheres per amino acid were used. It could represent the conformation of the 82 proteins in an independent test set with the mean and standard deviation RMSD of 1.01 and 0.09 A, respectively, based on the position of alpha carbons and the centers of mass of sidechains.