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PubMed1988

[Computer aided design of anticancer drugs].

The recent advances in computer science and technology enabled us to use computer for drug-design. Calculation of structural features of drugs and modeling of biomacromolecules by means of 3D-computer graphics afford a new approach to comprehend a molecular interaction which is important for drug action. As target molecules for anticancer drug, DNA structure can be elucidated and drug-DNA complex model can be constructed to give further insight for drug design. For example, complex of DNA double helix and bleomycin was built and by conjunction with other complex model such as mitomycin C, anthramycin, and netropsin it would be able to design a base sequence specific DNA-groove binding molecule. In addition, DNA is also a target molecule for antibiotics which intercalate between base pairs. Rational design of intercalator and groove binder thus would lead a novel anticancer drug. On the other hand, combination of the fruitful results of molecular biology and gene engineering with computer technology, will give a detail of protein structure which is one of most desired information for designing novel drugs.

Antineoplastic Agents↗
PubMed1981

A computer-generated three-dimensional model of the B chain of bovine alpha-thrombin.

A computer graphic molecular display system has been used to construct a three-dimensional model of the B chain of bovine thrombin. The model is derived from the bovine alpha-chymotrypsin structure as determined by X-ray crystallographic studies. The amino acid sequence of bovine thrombin has been substituted for that of alpha-chymotrypsin, preserving the beta-barrel structure and maximizing homology of the amino acid sequence of the two proteins. With the exception of an area in the vicinity of the specificity binding pocket, most of the changes observed in thrombin occur on the surface of the molecule. The most notable changes observed in the model are the increases on the surface of positively charged (arginine and lysine) and negatively charged (glutamate and aspartate) residues. A glutamate replaces methionine 192 near the entrance to the specificity binding pocket. The nature of this site was further altered by the substitution of an aspartate for serine 189 and an alanine for serine 190. The structure of the resulting specificity binding pocket is consistent with that of serine proteases, which have trypsin-like substrate specificity. The computer graphics molecular display system has been used to insert models of synthetic thrombin inhibitors into the active site of the thrombin B chain model. With the model, it has been possible to correlate the interaction of thrombin with the observed binding constants of two inhibitors of trypsin-like serine proteases, p-amidinophenylmethylsulfonylfluoride (Ki = 1.27 x 10(-6) M) and m-[m-(trifluoromethyl)phenoxypropoxy]benzamidine (KD = 2.9 x 10(-6) M).

Amino Acids↗
PubMed1992

The structural mimicry of membrane sterols by tamoxifen: evidence from cholesterol coefficients and molecular-modelling for its action as a membrane anti-oxidant and an anti-cancer agent.

The anti-cancer drug tamoxifen is a potent inhibitor of lipid peroxidation induced by Fe(III)-ascorbate in ox-brain phospholipid liposomes. Similar anti-oxidant effects, but with varying potencies, are also shown by 4-hydroxy-tamoxifen, cholesterol, ergosterol and 17-beta-oestradiol. We now describe a computer-graphic fitting technique that demonstrates a structural similarity between the five compounds. In addition, we have quantified the differences (relative to cholesterol) between the anti-oxidant activities of the compounds in terms of a novel expression referred to here as the cholesterol coefficient (Cc) Finally, we discuss how the inhibitory effect of tamoxifen on lipid peroxidation may result from a membrane stabilization that is associated with a decrease in membrane fluidity. This action may be related to the anti-proliferative effect exerted by tamoxifen on cancer and fungal cells.

Antifungal Agents↗
PubMed1988

The Escherichia coli 30S ribosomal subunit; an optimized three-dimensional fit between the ribosomal proteins and the 16S RNA.

We have generated a computerized fit between the 3-dimensional map of the E.coli 30S ribosomal proteins, as determined by neutron scattering, and the recently published 3-dimensional model for the 16S RNA. To achieve this, the framework of coordinates for RNA-protein cross-link sites on the phosphate backbone in the RNA model was related to the corresponding framework of coordinates for the mass centres of the proteins by a least squares fitting procedure. The resulting structure, displayed on a computer graphics system, gives the first complete picture of the E.coli 30S ribosomal subunit showing both the proteins and the double-helical regions of the RNA. The root mean square distance between cross-link sites and protein centres is 32 A. The position of the mass centre of the combined double-helical regions was calculated from the model and compared with the position of the mass centre of the complete set of proteins. The two centres are displaced relative to one another by 20 A in the model structure, in good agreement with the experimental value of 25 A found by neutron scattering.

Computer Graphics↗
PubMed1983

A computer graphic-based angiographic model for normal left ventricular contraction in man and its application to the detection of abnormalities in regional wall motion.

Analyzing the digitized left ventricular cineangiograms of 70 patients with no demonstrable heart disease (NDHD), we derived an angiographic model for normal contraction in the intact heart as viewed in the 30 degree right anterior oblique projection. This model was verified statistically by comparing the predicted regional stroke volumes with the measured volumes for the NDHD group. A wall motion system based on this model was compared with four other systems by examining the ventriculograms of 141 patients, all suffering from coronary artery disease but with normal volumes and ejection fractions (greater than 0.61). Of these, 60 had normally contracting ventricles and 81 exhibited mild regional abnormalities according to two experienced angiographers. Using Cochrane's Q test, we found significant differences among the five methods (Q = 29.5;p less than .001). The new approach showed significantly better agreement with the subjective assessment than the next best method (Q = 5.3;p less than .05). On a regional basis, overall sensitivity was 87.5% and specificity was 97.9%.

Adult↗
PubMed1989

Assessment of feature size abnormalities using receiver operating characteristic analysis.

The ability of an observer to detect variations in size of a geometrical image feature have been investigated using receiver operating characteristic (ROC) analysis. Three types of image were constructed using computer graphics: disc-shaped targets of variable radius, model chest radiographs showing a variable heart diameter and model arterial angiograms with variable vessel width. Five factors were investigated: observer experience, variation of detectability with theoretical signal-to-noise ratio, the prior probability of the presence of an abnormality, viewing distance, and uncertainty in the location of an abnormality. In all but one experiment, excellent agreement was found between measured detectabilities and the predictions of signal detection theory, providing an initial practice session was included for each observer. No significant variation in detectability was found using six different prior probabilities and two different viewing distances, and the reduction in detectability for a four-alternative location task was in good agreement with theoretical predictions. The high statistical efficiencies found for the detection of geometrical signals suggest that the levels of observer "internal" noise arising from decision-making processes during an ROC experiment are very low.

Computer Graphics↗
PubMed1988

Crystal structure of p-hydroxybenzoate hydroxylase complexed with its reaction product 3,4-dihydroxybenzoate.

Crystals of the flavin-containing enzyme p-hydroxybenzoate hydroxylase (PHBHase) complexed with its reaction product were investigated in order to obtain insight into the catalytic cycle of this enzyme involving two substrates and two cofactors. PHBHase was crystallized initially with its substrate, p-hydroxybenzoate and the substrate was then converted into the product 3,4-dihydroxybenzoate by allowing the catalytic reaction to proceed in the crystals. In addition, crystals were soaked in mother liquor containing a high concentration of this product. Data up to 2.3 A (1 A = 0.1 nm) were collected by the oscillation method and the structure of the enzyme product complex was refined by alternate restrained least-squares procedures and model building by computer graphics techniques. A total of 273 solvent molecules could be located, four of them being presumably sulfate ions. The R-factor for 14,339 reflections between 6.0 A and 2.3 A is 19.3%. The 3-hydroxyl group of the product introduced by the enzyme is clearly visible in the electron density, showing unambiguously which carbon atom of the substrate is hydroxylated. A clear picture of the hydroxylation site is obtained. The plane of the product is rotated 21 degrees with respect to the plane of the substrate in the current model of enzyme-substrate complex. The 4-hydroxyl group of the product is hydrogen bonded to the hydroxyl group of Tyr201, its carboxyl group is interacting with the side-chains of Tyr222, Arg214 and Ser212, while the newly introduced 3-hydroxyl group makes a hydrogen bond with the backbone carbonyl oxygen of Pro293.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed1995

Analysis of action of the wobble adenine on codon reading within the ribosome.

Computer graphics simulation of the interaction between the codon-anticodon duplexes containing adenine in the first (wobble) position of the anticodons, and bound to the ribosomal A- and P-sites, was made. This demonstrated that widespread use of adenine in the wobble position in anticodons should lead to a low efficiency of ribosomal translation, since the wobble A of the P-site tRNA weakens the codon-dependent binding of aminoacyl-tRNA at the A-site via interduplex interaction. Besides the canonical partner U, the wobble A of aminoacyl-tRNA can recognize A, C, G in the third position of the codon by the formation of the propeller twist in the wobble pairs AA, AC, AG. The conversion of the wobble A into inosine improves its pairing with the codon bases (the pairs IA and IC, unlike AA and AC, should not form the propeller twist leading to the deformation of base-base hydrogen bonds) and should reduce an adverse effect of the P-site wobble adenine on the formation of the A-site duplex. The consequence of the interaction between the ribosomal P- and E-site duplexes has been formulated. According to this the E-site wobble A should enhance the probability of frameshifting. These properties of the wobble A and I could be a reason why A is very rarely observed in the first anticodon position and why evolutionary processes have developed the enzyme which modifies the wobble A to I. The results obtained can be subjected to direct experimental tests.

Adenine↗
PubMed1991

Reliability of cephalometric analysis using manual and interactive computer methods.

This study compares the results of cephalometric analyses using manual and interactive computer graphics methods. Results are statistically in favour of the interactive computer system. This study provides a basis for ongoing research into alternative methods of cephalometric analyses, such as digitization and automatic landmark identification using sophisticated computer vision systems.

Cephalometry↗
PubMed1988

The modelling of nucleophilic and electrophilic additions to organometallic complexes using molecular graphics techniques.

A new formalism has been developed in order to evaluate intermolecular interaction energies for inorganic and organometallic complexes in the framework of the extended Hückel method. In order to provide the shortest possible response time on an interactive computer graphics facility, this model should require the minimum amount of computer time, which explains why approximate procedures are used to evaluate electrostatic, charge transfer and exchange repulsion components. When applying this model to typical examples of electrophilic addition reactions to organometallic complexes, it is found that it is essential to take account of charge transfer interactions, the electrostatic component alone being not sufficient, even qualitatively, for a proper description of the reaction mechanism. The results, presented as color-coded dot molecular surfaces, show a very good agreement with experiment as to the site of attack, namely (i) on metal for the electrophilic attack on Fe(cp)2, Fe(CO)5 and X(cp)(CO)2, X = Co, Rh; (ii) on the cp ligand for the nucleophilic attack on Co(cp)2+ and Rh(cp)2+; (iii) on bz for the nucleophilic attack on Fe(cp)(bz)+. Finally, modellizations of the nucleophilic attack on a coordinated olefin and of the relation between structure and acidic properties of zeolites are presented and discussed.

Computer Graphics↗
PubMed1991

A veterinary digital anatomical database.

This paper describes the Veterinary Digital Anatomical Database Project. The purpose of the project is to investigate the construction and use of digitally stored anatomical models. We will be discussing the overall project goals and the results to date. Digital anatomical models are 3 dimensional, solid model representations of normal anatomy. The digital representations are electronically stored and can be manipulated and displayed on a computer graphics workstation. A digital database of anatomical structures can be used in conjunction with gross dissection in teaching normal anatomy to first year students in the professional curriculum. The computer model gives students the opportunity to "discover" relationships between anatomical structures that may have been destroyed or may not be obvious in the gross dissection. By using a digital database, the student will have the ability to view and manipulate anatomical structures in ways that are not available through interactive video disk (IVD). IVD constrains the student to preselected views and sections stored on the disk.

Anatomy, Veterinary↗
PubMedDate not supplied

Using greyscale voxel databases for improved shading and segmentation.

Many different data representations are possible in computer graphics. Originally, in the medical field, simplified methods were used in order to reduce computation times on small computer systems. Currently a wider range of techniques is developing as costs of hardware continue to fall. In this paper we review a number of possible representations and explain the advantage of one that is greyscale, volumetric and random access. Different segmentation techniques can be used, as well as shading algorithms that give greatly improved appearances. A quantitative analysis of shading methods is derived in terms of the degree of sampling of the 'pseudo-normal' vectors that estimate the direction of the tangent to a surface. The application to a study of multiple sclerosis lesions in the brain using nuclear magnetic resonance data is shown.

Brain↗
PubMed1992

Designing a user interface and computer screens for instruction: some considerations.

Computer-assisted instruction and interactive videodisc are being used more often in allied health sciences education and medical training. Because computer graphics screens can enhance both legibility and readability, an effective computer interface for instruction is basic to the design and development of both. This article discusses guidelines on legibility, which includes the use of graphics, type and text, contrast, and color.

Color↗