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We have developed a special-purpose computer for computational fluid dynamics, DREAM-1A. DREAM-A has a peak speed of 80 Mflops and a memory size of 1.6 Gbyte. DREAM-1A consists of four units connected in a one-dimensional bidirectional ring network. One unit of DREAM-1A has one vector processing unit (VPU) and one hard-disk unit. The physical variables are stored in hard disk, instead of RAM. The...
Many quantitative structure-activity relationships (QSARs) have been published in pure organic chemistry as well as from biological sources since 1935 when Hammett introduced his equation. We have organized a database of about 6,000 QSARs about evenly divided from both sources. We discuss how the database can be searched for different types of QSAR and how this facilitates comparison of new QSARs...
Introduces a class of recursively-based computational methods for studying the statistical physics of lattice polymer systems. The methods display certain novel aspects geared specifically towards the efficient analysis of lattice heteropolymer models at low temperatures. However, the general principles are in fact extremely general in scope, and can be applied also to problems at arbitrary temperatures,...
Matrices of intraglobular contacts and vectors of coordination numbers derived from the amino acid sequence form the basis for computer procedures for the analysis and prediction of the tertiary structure of proteins. Three main modules perform: 1) prediction of the plot of residue-coordination numbers (number of contacts) on the basis of amino-acid sequence; 2) calculation of the matrix of intraglobular...
A residue-residue interaction pseudo-potential has been developed specific for protein /spl beta/-sheets. The potential is derived by scoring the occurrence of all i-(j-2...J+2) residue-residue pairs between any two interacting /spl beta/-strands, subdividing according to 4 classes of hydrogen bond pattern. The potential can be useful in distinguishing between correct and incorrect alignments between...
A genetic algorithm is used to search energetically and structurally favorable conformations. The authors use a hybrid protein representation, three operators to manipulate the protein "genes" and a fitness function based on a simple force field. The prototype was applied to the ab initio prediction of Crambin. None of the conformations generated with a non-biased fitness function are similar...
Proposes novel prediction schemes for protein 3D structure prediction that include both local and global factors of protein structure formation. The authors have developed a powerful description scheme for protein conformation, MLD (Multi-Level Description) in order to model the protein structure formation. In this scheme, the description is reconstructable into the three-dimensional conformation...
Presents a new branch-and-bound method of searching the space of possible "threadings" for the optimal match of a sequence to an adjacency matrix of environments in the "motif threading" version of the "inverse protein folding problem." The method is guaranteed to find the optimal threading first, and thereafter will enumerate successive candidate threadings in order...
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