Analysis and prediction of primary structures of proteins using a computer

On the basis of a computer analysis of four classes of toxic polypeptides, generalized primary structures of each class have been obtained which can be used for planning the synthesis of biologically active compounds.Institute of Biochemistry, Uzbek SSR Academy of Sciences, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, Vol. 6, pp. 822–830, November–December, 1989.     

De novo prediction of the structures of M. tuberculosis membrane proteins

The structures of four integral membrane proteins from the Mycobacterium tuberculosis (TB) gene, Rv2433c, Rv1861, Rv1616, and Rv3069, have been de novo predicted by combining a generalized Born implicit solvent/membrane model with replica exchange molecular dynamics simulations to sample the conformational space of each protein.     

The prediction of inorganic crystal framework structures using excluded regions within a genetic algorithm approach

We have developed a new technique, which is complementary to other procedures, that will have wide applicability for generating new feasible framework structures with defined microporous architectures from the knowledge of only the unit cell dimensions, constituent elements and by defining forbidden regions within the unit cell.     

Management of radioactive wastes using a personal computer

This paper describes a software package for a personal computer which deals with storage records of radioactive wastes; the software keeps the records of purchase and use of radioisotopes and makes the inventory records of radioactive wastes. The records for the cargo booking of the wastes for the Japanese Radioisotope Association can be prepared by this software package.     

Computational design and prediction of interesting not-yet-synthesized structures of inorganic materials by using building unit concepts

The computational design of new and interesting inorganic materials is still an ongoing challenge. The motivation of these efforts is to aid the often difficult task of crystal structure determination, to rationalize different but related structure types, or to help limit the domain of structures that are possible in a given system. Over the past decade, simulation methods have continuously evolved towards the prediction of new structures using minimal input information in terms of symmetry, cell parameters, or chemical composition. So far, this task of identifying candidate structures through an analysis of the energy landscape of chemical systems has been particularly successful for predominantly ionic systems with relatively small numbers of atoms or ions in the simulation cell. After an introductory section, the second section of this work presents the historical developments of such simulation methods in this area. The following sections of the work are dedicated to the introduction of the building unit concept in simulation methods: we present simulation approaches to structure prediction employing both primary (aggregate of atoms) and secondary (aggregate of coordination polyhedra) building units. While structure prediction with primary units is a straightforward extension of established approaches, the AASBU method (automated asssembly of secondary building units) focusses on the topology of network-based structures. This method explores the possible ways to assemble predefined inorganic building units in three-dimensional space, opening the way to the manipulation of very large building units (up to 84 atoms in this work). As illustrative examples we present the prediction of candidate structures for Li(4)CO(4), the identification of topological relationships within a family of metalphosphates, ULM-n and MIL-n, and finally the generation of new topologies by using predefined large building units such as a sodalite or a double-four-ring cage, for the prediction of new and interesting zeolite-type structures.     

Analysis of DTA curves and calculation of kinetic data using computer technique

Principles of two computer programs useful for the evaluation of heterogeneous kinetics are described.The first program ALANTA allows to obtain the non-isothermal kinetic curve from the shape of general DTA peak using the DTA-equation derived elsewhere¹.The second program SQUEST determines the kinetic mechanism which is the most appropriate to a given non-isothermal kinetic curve and evaluates the corresponding kinetic parameters. The program decides between 19 kinetic models and uses both integral and differential methods of evaluation.     

Analytical calculations using a computer in molecular spectroscopy

The paper deals with the discussion of problems of calculating the vibration-rotation energy and wave functions of polyatomic molecules using systems for analytical calculations. The system developed can be used for obtaining the analytical expressions for the spectroscopic parameters which are useful for solving both the direct and inverse spectroscopic problems.     

Analysis of amino acids and proteins using a poly(methyl methacrylate) microfluidic system

Plastic microchips are very promising analytical devices for the high-speed analysis of biological compounds. However, due to its hydrophobicity, their surface strongly interacts with nonpolar analytes or species containing hydrophobic domains, resulting in a significant uncontrolled adsorption on the channel walls. This paper describes the migration of fluorescence-labeled amino acids and proteins using the poly(methyl methacrylate) microchip. A cationic starch derivative significantly decreases the adsorption of analytes on the channel walls. The migration time of the analytes was related to their molecular weight and net charge or pI of the analytes. FITC-BSA migrated within 2 min, and the theoretical plate number of the peak reached 480,000 plates/m. Furthermore, proteins with a wide range of pI values and molecular weights migrated within 1 min using the microchip.     

Performance of the updated inaa advance prediction computer program

This paper describes further development and experimental testing of the INAA Advance Prediction Computer Program (APCP). Copies of the APCP written in BASIC-PLUS are finally ready for distribution. Experimental tests with four reference materials are described. The program is extremely useful as a quide to optimum conditions, sample sizes, elements detectable, and INAA lower limits, of detection for any sample matrix of only approximately known major and minor elemental composition. Additional developments in progress are mentioned.     

Analysis and prediction of hydrogen bonding in protein-DNA complexes using parallel processors

A number of essential biological functions are controlled by proteins that bind to specific sequences in genomic DNA. In this article we present a simplified model for analyzing DNA-protein interactions mediated exclusively by hydrogen bonds. Based on this model, an optimized algorithm for geometric pattern recognition was developed. The large number of local energy minima are efficiently screened by using a geometric approach to pattern matching based on a square-well potential. The second part of the algorithm represents a closed form solution for minimization based on a quadratic potential. A Monte Carlo method applied to a modified Lennard-Jones potential is used as a third step to rank DNA sequences in terms of pattern matching. Using protein structures derived from four DNA-protein complexes with three-dimensional coordinates established by X-ray diffraction analysis, all possible DNA sequences to which these proteins could bind were ranked in terms of binding energies. The algorithm predicts the correct DNA sequence when at least two hydrogen bonds per base pair are involved in binding to the protein, providing a partial solution to the three-dimensional docking problem. This study lays a framework for future refinements of the algorithm in which the number of assumptions made in the present analysis are reduced. © 1996 by John Wiley & Sons, Inc.     

New forms of the INAA advance prediction computer program

The development and experimental testing of a new instrumental neutron activation analysis (INAA) Advance Prediction Computer Program (APCP) is described for activation by high-intensity, short-duration reactor pulses. Also presented are the results of extensive experimental testing of the APCP for epithermal INAA. Brief mention is made of other forms of the APCP not yet completed, but in various stages of development.     

Analysis and prediction of protein folding rates using quadratic response surface models

Understanding the relationship between amino acid sequences and folding rates of proteins is an important task in computational and molecular biology. In this work, we have systematically analyzed the composition of amino acid residues for proteins with different ranges of folding rates. We observed that the polar residues, Asn, Gln, Ser, and Lys, are dominant in fast folding proteins whereas the hydrophobic residues, Ala, Cys, Gly, and Leu, prefer to be in slow folding proteins. Further, we have developed a method based on quadratic response surface models for predicting the folding rates of 77 two- and three-state proteins. Our method showed a correlation of 0.90 between experimental and predicted protein folding rates using leave-one-out cross-validation method. The classification of proteins based on structural class improved the correlation to 0.98 and it is 0.99, 0.98, and 0.96, respectively, for all-alpha, all-beta, and mixed class proteins. In addition, we have utilized Baysean classification theory for discriminating two- and three-state proteins, which showed an accuracy of 90%. We have developed a web server for predicting protein folding rates and it is available at http://bioinformatics.myweb.hinet.net/foldrate.htm.     

Design of a superhydrophobic surface using woven structures

The relationship between surface tension and roughness is reviewed. The Cassie-Baxter model is restated in its original form, which better describes the most general cases of surface roughness. Using mechanical and chemical surface modification of nylon 6,6 woven fabric, an artificial superhydrophobic surface was prepared. A plain woven fabric mimicking the Lotus leaf was created by further grafting 1H,1H-perfluorooctylamine or octadecylamine to poly(acrylic acid) chains which had previously been grafted onto a nylon 6,6 woven fabric surface. Water contact angles as high as 168 degrees were achieved. Good agreement between the predictions based on the original Cassie-Baxter model and experiments was obtained. The version of the Cassie-Baxter model in current use could not be applied to this problem since the surface area fractions in this form is valid only when the liquid is in contact with a flat, porous surface. The angle at which a water droplet rolls off the surface has also been used to define a superhydrophobic surface. It is shown that the roll-off angle is highly dependent on droplet size. The roll-off angles of these superhydrophobic surfaces were less than 5 degrees when a 0.5 mL water droplet was applied.     

Molecular parameters for the prediction of polyurethane structures

Recent efforts to determine the structures of poly(MDI/diol) hard segments in polyurethane elastomers have relied on the structures determined by single-crystal x-ray methods for diphenylmethane urethane model compounds. We have surveyed the structure of six model compounds, and have derived average values for the bond lengths, bond angles, and bond torsion angles for use in future analyses. The applicability of these averages to polymer structures is discussed, and the data are used to derive models for the poly(MDI-butanediol) chain which are found to be consistent with the fiber repeat determine by x-ray methods.