I. N. Shindyalov, W. Chang, J. A. Cooper, P. E. Bourne
The broad goal of our work has been to design, im-plement, and now begin to use an extensible object oriented framezwork which represents biological macro-molecules and,which can be queried in...
P. E. Bourne, W. Krebs, W. Li, I. N. Shindyalov, Z. Ghahramani, ...
Structural genomics – large-scale macromolecular 3-dimenional structure determination – is unique in that major participants report scientific progress on a weekly basis. The target database...
A case study of high-throughput biological data processing on parallel platforms (2004)
Pekurovsky, D., Shindyalov, I. N., Bourne, P. E.
Motivation: Analysis of large biological datasets using a variety of parallel processor computer architectures is a common task in bioinformatics. The efficiency of the analysis can be significantly...
A case study of high-throughput biological data processing on parallel platforms (2004)
Pekurovsky, D., Shindyalov, I. N., Bourne, P. E.
Motivation: Analysis of large biological data sets using a variety of parallel processor computer architectures is a common task in bioinformatics. The efficiency of the analysis can be significantly...
A case study of high-throughput biological data processing on parallel platforms (2004)
Pekurovsky, D., Shindyalov, I. N., Bourne, P. E.
Motivation: Analysis of large biological datasets using a variety of parallel processor computer architectures is a common task in bioinformatics. The efficiency of the analysis can be significantly...
C. Guda, E. D. Scheeff, P. E. Bourne, I. N. Shindyalov
We have developed a new algorithm for the alignment of multiple protein structures based on a Monte Carlo optimization technique. The algorithm uses pair-wise structural alignments as a starting...
C. Guda, E. D. Scheeff, P. E. Bourne, I. N. Shindyalov
We have developed a new algorithm for the alignment of multiple protein structures based on a Monte Carlo optimization technique. The algorithm uses pair-wise structural alignments as a starting...
C. Guda, E. D. Scheeff, P. E. Bourne, I. N. Shindyalov
We have developed a new algorithm for the alignment of multiple protein structures based on a Monte Carlo optimization technique. The algorithm uses pair-wise structural alignments as a starting...
Design and application of PDBlib, a C++ macromolecular class library (1994)
Chang, W., Shindyalov, I.N., Pu, C., Bourne, P.E.
PDBlib is an extensible object-oriented class library written in C++ for representing the three-dimensional structure of biological macromolecules. The software design strategy, features of many of...
Shindyalov, I.N., Kolchanov, N.A., Sander, C.
A method has been developed to detect pairs of positions with correlated mutations in protein multiple sequence alignments. The method is based on reconstruction of the phylogenetic tree for a set of...
Macromolecular query language (MMQL): prototype data model and implementation (1994)
Shindyalov, I. N., Chang, W., Pu, C., Bourne, P.E.
Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological...
PDBTool: A Prototype Object Oriented Toolkit for Protein Structure Verification (1992)
C. Pu, Pu Sheka Ong, J. Ong, L. Chang, A. Chang, E. Alessio, ...
The Protein Data Bank (PDB) is a large and rapidly growing standard repository of complex biological macromolecules. Existing software tools for the PDB, including storage management, are quite...
Streletc, V.B., Shindyalov, I.N., Kolchanov, N.A., Milanesi, L.
We present a new pairwise alignment algorithm that uses iterative statistical analysis of homologous subsequences. Apart from the classical conversion of the DOT-matrix characteristic of the...
Tsigelny, I., Shindyalov, I. N., Bourne, P. E., Südhof, T. C., Taylor, P.
Comparisons of protein sequence via cyclic training of Hidden Markov Models (HMMs) in conjunction with alignments of three-dimensional structure, using the Combinatorial Extension (CE) algorithm,...