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At least 991 records · Page 55Linked to original sources
PubMed1996

Beyond the hyperactive molecule: search, salvage and visualization of chemical information from the Internet.

The established exchange mechanisms for chemical information are under attack from new information distribution channels on the Internet. Increasingly chemical information is distributed by means of WWW pages and similar media. However, most of this information is still primarily intended for human browsing. The search for chemical information and the reuse of encoded structures and their attached data is complicated and often impossible because of the unorganized structure of the information and the lack of tools for search, display and salvage of chemical information to help with the extraction of reusable information from Webspace. The situation is complicated by the lack of standards and formats powerful enough to encode in computer-readable form sophisticated chemical information and informational relationships. The rapid evolution of information exchange mechanisms on the Internet is another problem. The unsettled situation demands a new generation of intelligent chemistry-aware tools for information retrieval from the Net. These tools must be capable of adapting to new trends and information models as well as new information types without constant redesign and should be themselves extendable and updatable by components distributed via the same network connections as the chemical data they are supposed to deal with. We introduce a set of tools which encapsulate the established Internet (especially WWW) information transfer and visualization methods and extend them to a new level of chemical information handling.

Chemistry↗
PubMed1997

Ubiquitous distributed objects with CORBA.

Database interoperation is becoming a bottleneck for the research community in biology. In this paper, we first discuss the question of interoperability and give a brief overview of CORBA. Then, an example is explained in some detail: a simple but realistic data bank of STSs is implemented. The Object Request Broker is the media for communication between an object server (the data bank) and a client (possibly a genome center). Since CORBA enables easy development of networked applications, we meant this paper to provide an incentive for the bioinformatics community to develop distributed objects.

Base Sequence↗
PubMed1997

Combinatorial tools for the analysis of transcriptional regulation.

In this paper, we discuss virtual experiments for the study of major regulatory processes such as translation, signalization or transcription pathways. An essential part of these processes is the formation of protein clusters held together by a small number of binding domains that can be shared by many different proteins. Analysis of these clusters is complicated by the vast number of different arrangements of proteins that can trigger a specific reaction. We propose combinatorial tools that can help predict the effects on the rate of transcription of either changes in transcriptional factors concentration, or due to the introduction of chimeras combining domains not usually present on a protein.

Computer Simulation↗
PubMed1997

Test tube systems with cutting/recombination operations.

We introduce test tube systems based on operations that are closely related to the splicing operation, i.e. we consider the operations of cutting a string at a specific site into two pieces with marking them at the cut ends and of recombining two strings with specifically marked endings. Whereas in the splicing of two strings these strings are cut at specific sites and the cut pieces are recombined immediately in a crosswise way, in CR(cutting/recombination)-schemes cutting can happen independently from recombining the cut pieces. Test tube systems based on these operations of cutting and recombination turn out to have maximal generative power even if only very restricted types of input filters for the test tubes are used for the redistribution of the contents of the test tubes after a period of cuttings and recombinations in the test tubes.

Alternative Splicing↗
PubMed1997

Organizing and computing metabolic pathway data in terms of binary relations.

A new database system named KEGG is being organised to computerize functional aspects of genes and genomes in terms of the binary relations of interacting molecules or genes. We are currently working on the metabolic pathway database that is composed of three interconnected sections: genes, molecules, and pathways, which are also linked to a number of existing databases through our DBGET retrieval system. Here we present the basic concept of binary relations and hierarchical classifications to represent the metabolic pathway data. The database operations are then defined as an extension of the relational operations, and the path computation problem is considered as a deduction from binary relations. An example of using KEGG for the functional prediction of genomic sequences is presented.

Animals↗
PubMed1997

Design of hydrophobic core of E. coli malate dehydrogenase based on the side-chain packing.

We have developed computational programs for the de novo design of hydrophobic cores of proteins. The first program optimizes side-chain conformations using an updated rotamer library for potential hydrophobic residues, based on the backbone structure of the protein of interest. The second program selects candidates to be engineered among the sequences by estimating changes in Gibbs free energy between the folded and unfolded structure of the proteins with new sequence. Using these programs, we constructed several variants of E. coli malate dehydrogenase (eMDH) which could have increased stability at 25 degrees C, compared to the wild type enzyme. To quantitate stability change between variants and the wild type, circular dichroism spectra were measured as a function of guanidine hydrochloride concentration at 25 degrees C, pH 7.0. This analysis showed that three variants constructed in this study were stabilized more than or equal to the wild type. This demonstrated that our programs may be powerful tools to design new proteins with high stability.

Amino Acid Sequence↗
PubMed1997

Towards a bacteriorhodopsin-silicon neuromorphic photosensor.

We describe our efforts towards constructing a hybrid protein-silicon neuromorphic photosensor based on the photo-active protein bacteriohodopsin. This protein displays an differential photosensitivity similar to the response of the receptive field of an X-type retinal ganglion cell. Similar bacteriohodopsin photoelectrode arrays display inherent edge detection and motion enhancement. We discuss challenges associated with constructing and understanding the protein-silicon interface and possible chemical solutions for our experimental device.

Animals↗
PubMed1997

Toward a virtual-labo-system for metabolic engineering: development of biochemical engineering system analyzing tool-kit (BEST-KIT).

BEST-KIT is an efficient and user-friendly "biochemical engineering system analyzing tool-kit" integrated the following key modules: 1) mathematical modeling and editing of reaction-scheme, 2) automatic derivation of differential equations, 3) numerical calculation, 4) nonlinear optimization, 5) visualization, 6) retrieve the information on reaction mechanism and kinetic parameters from data-base of metabolic pathways. The users of this simulator are assumed to be unfamiliar with computer technology and with computer programming. The integrated interface (UNIX version) is based on Xlib, XToolkit and OSF/Motif Widget.

Biochemistry↗
PubMed1997

Real time surface reconstruction for moving molecular fragments.

Recently we introduced the Reduced Surface as an efficient tool to built molecular surfaces. We describe here how this geometric construct can be used to efficiently reconstruct the solvent excluded surface of a protein for which the coordinates of a subset of atoms are changing. We show that, the complexity of that operation is not dependent upon the size of the molecule and is in O[tlog(t)] where t is the maximum of the number of probes and atoms involved in the reconstruction of the surface. The algorithms described here have been implemented and tested on several proteins. The triangulation of the solvent excluded surface of proteins in which a side chain was changing conformation could be updated at rates ranging from 7 to 22 frames per second. We also applied this method to compute the surface area fluctuation of the FIV protease undergoing a constrained molecular dynamics simulation (16 mobile residues). Rate of 6 frames per second were obtained in this case.

Algorithms↗
PubMed1997

Enumerating suboptimal alignments of multiple biological sequences efficiently.

The multiple sequence alignment problem is very applicable and important in various fields in molecular biology. Because the optimal alignment that maximizes the score is not always biologically most significant, providing many suboptimal alignments as alternatives for the optimal one is very useful. As for the alignment of two sequences, this suboptimal problem is well-studied, but for the alignment of multiple sequences, it has been considered impossible to investigate such suboptimal alignments because of the enormous size of the problem. The optimal multiple alignment can be obtained with A* algorithm, and an efficient algorithm for the k shortest paths problem on general graphs is discovered recently. We extend these algorithms for computation of set of all aligned groups of residues in optimal and suboptimal alignments, and for enumeration of suboptimal alignments. The suboptimal alignments are numerous. Thus we discuss what kind of suboptimal alignment is unnecessary to enumerate, and propose an efficient technique to enumerate only necessary alignments. The practicality of these algorithms are demonstrated through experiments. Moreover, the property of suboptimal alignments of multiple sequences are also examined through experiments.

Algorithms↗
PubMed1996

Relationship between various functional impression techniques and different operators.

The purpose of the present investigation was to determine the relationship between the reproducibility of soft tissue contours by three different functional impression techniques and four dentists for mandibular distal-extension removable partial dentures. The selected functional impression methods were Lejoyeux, Rouot and McLean techniques. A mucostatic impression technique was used for the control group. To compare and measure the degree of tissue displacement, a three-dimensional coordinate measuring system was used. The differences in vertical displacement of soft tissue among the operators were statistically determined for each impression technique used. Lejoyeux technique produced the least variation in tissue displacement followed respectively by McLean, mucostatic and Rouot methods.

Computing Methodologies↗
PubMed1998

Bidirectional sticker systems.

We introduce two-sided sticker systems, the two-sided variant of a computability model introduced as an abstraction of Adleman's style of DNA computing and of the matching of the so-called Watson-Crick complements. Several types of sticker systems are shown to have the same power as regular grammars, one variant is found to represent the linear languages, and another one is proved to be able to represent any recursively enumerable language. From this result we infer that any recursively enumerable language can be represented as the projection of the intersection of two minimal linear languages.

Base Composition↗
PubMed1998

Finite H-systems with 3 test tubes are not predictable.

Finite H-systems with n test tubes are splicing systems of n test tubes over a common molecular alphabet, sigma, with a filter Fi [symbol: see text] sigma for each test tube. Initially, arbitrary many copies of molecules and enzymes (splicing rules) from a finite set of molecules and enzymes are given to the test tubes that produce new molecules by splicing and filtering. It is known that any formal language can be generated by a finite H-system with 9 test tubes and that the results of finite H-systems with 6 test tubes are unpredictable. Here we present a rather simple proof that the results of finite H-systems with only 3 test tubes are unpredictable and that 4 test tubes suffices to generate any formal language.

Algorithms↗
PubMed1998

Is the hippocampus a Kalman filter?

Based on a large body of neurophysiological, neuroanatomical, and behavioral data, it has been suggested that the hippocampal formation serves as a spatial learning and localization system. This spatial representation is metric in nature and arises as a result of associations between sensory inputs and dead-reckoning information generated by the animal. However, despite the fact that these two information streams provide uncertain information (e.g., recognition errors, dead-reckoning drifts, etc.), the hippocampal computational models suggested to date have not explicitly addressed information fusion from erroneous sources. In this paper we develop a computational model of hippocampal spatial learning and relate its functioning to a probabilistic tool used for uncertain sensory fusion in robots: the Kalman filter. This parallel allows us to derive statistically optimal update expressions for the localization performed by our computational model.

Animals↗