Biomedical subjects

E Furuichi

Publications and source records attributed to E Furuichi.

7 recordsLinked to original sources

PubMed1998

Influence of protein structure databases on the predictive power of statistical pair potentials.

A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 A). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing alpha-proteins will only perform best on alpha-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database.

Chemical Phenomena↗

PubMed1997

Application of a deductive database system to search for topological and similar three-dimensional structures in protein.

A deductive database system PACADE (Protein Atomic Coordinate Analyzer with Deductive Engine) has been developed for protein structure analysis. With this system, super-secondary structures described in logical and declarative rules can be retrieved effectively. For protein structure analysis, comparison of local structures in different proteins is a necessary mean. A function to search for similar structures has, therefore, been added to the PACADE system. We describe herein the result of searches for the same topological structures and three-dimensionally similar ones. A user of PACADE can select these two levels of similarity by changing parameters. This function enables the inference system to retrieve similar structures, according to the restraints of variables defined by the user. Similar super-secondary structures among proteins can be searched for automatically, which is useful for protein structure analysis. The retrieved similar super-secondary structures can serve as criteria for protein spatial alignment.

Algorithms↗

PubMed1997

Extraction of substructures of proteins essential to their biological functions by a data mining technique.

Correlation between the sequential, structural, and functional features of proteins is one of the most important open questions in the field of molecular biology. To this problem, we apply a technique known as data mining for discovering associations across protein sequence, structure, and function. We were able to find various association rules on the substructures essential to some protein functions. Moreover, structure-structure associations were found between proteins having different functions. The results suggest that data mining might be a powerful tool in protein analysis.

Algorithms↗

PubMed1997

Finding association rules on heterogeneous genome data.

A novel approach for discovery of knowledge from genome data, which has been recently watched with interest in the research area of database, is applied to finding unified rules spreading over sequence, structure, and function of protein. As the result of experiments using data extracted from PDB, SWISS-PROT, and PROSITE, some association rules stating sequential/structural/functional aspects of two kinds of endopeptidases were found.

Computer Simulation↗

PubMed1996

Development and validation of TMJ viscoelasticity analyzer.

We developed a TMJ viscoelasticity analyzer for non-invasive evaluation of the soft tissues of the TMJ region. We used this device to measure the viscoelastic parameters, viscosity (c), elasticity (k) and mass (m), of the TMJ region for two volunteers. Experiments were performed to determine the optimum measurement conditions for the preload magnitude, head posture and clenching level. We determined measurement variability and carried out statistical analysis by analysis of variance (ANOVA). We found that the values for c and k varied significantly depending on preload magnitudes (p < 0.001). In addition, all parameters varied significantly depending on head posture. However, clenching level did not significantly affect any of the parameters. Measurement variability was below 10% for all parameters. Examination of viscoelasticity of the TMJ region provides valuable information about functional and pathological changes in the soft tissues of this area. In this study, we were able to determine the fundamental characteristics of the TMJ viscoelasticity analyzer and develop methods for examining patients with temporomandibular disorders.

Analysis of Variance↗

PubMed1995

Differences in MHC class I self peptide repertoires among HLA-A2 subtypes.

To investigate how single amino acid substitutions in MHC class I molecules affect differences in peptide repertoires, we eluted and sequenced the naturally processed peptides from three HLA-A2 subtypes (HLA-A*0204, -A*0206, and -A*0207) that differ by a single amino acid residue substitution each with HLA-A*0201 at the floor of the binding groove. Allele-specific peptide motifs for each HLA-A2 subtype substantially differed from that of HLA-A*0201 in the dominant anchor residues. The relative signal intensities for 18 self peptides, determined by mass spectrometry, precisely reflected these peptide motifs. Some overlapping peptides were isolated from both HLA-A*0201 and a single HLA-A2 variant, but no peptide was ubiquitously found across all variants. To rationalize the differences in peptide motifs, possible conformations of each allele were computer modeled by energy minimization calculations based on the reported crystal structure of HLA-A*0201. According to our models, the differences in peptide motifs could be explained by substituted-residue-driven conformational changes for each MHC-peptide complex. These results demonstrate the fine differences between HLA-A2 subtype self peptide repertoires and contribute to the prediction of antigenic peptides.

Amino Acid Sequence↗

PubMed1993

A deductive database system PACADE for analyzing 3-D and secondary structures of protein.

We have developed a deductive database system PACADE for analyzing 3-D and secondary structures of protein. The PACADE system consists of a relational database created from Protein Data Bank and a deductive engine DEE based on logic programming. It has the following features: (1) The system has an inference mechanism. This means by which users can easily write and check biological hypotheses using logical and declarative rules instead of procedural programs. (2) The relational database of the PACADE system stores data on both 3-D and secondary structures of protein. The integration of this two level structure makes feasible an abstract representation of the protein structure. We describe herein the design, functions, and implementation of this PACADE system.

Computer Graphics↗