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Ilya N. Shindyalov, Ph.D. Group Leader
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PROJECTS:
·
POM - Property Object Model. 1997-2006.
·
SPAM - Systematic Protein Annotation and Modeling.
2002-2007.
·
A
new scoring function and associated statistical significance for structure
alignment. 2003-2004.
·
pDomains - Definition and assignment of
structural domains in proteins. 2002-2006.
·
SPDC - Structural Protein Domain Classifications.
2002-2005.
·
EOL – Encyclopedia of Life – annotation
of complete genomes. 2002-2004.
·
PDP – Protein Domain Parser. 2002.
·
PAT - Structural and functional attotation
of Proteins of Arabidopsis thaliana. 2000-2002.
·
DMAPS - Multiple structure
alignment using Monte-Carlo approach. 1999-2001.
·
Analysis of common
subdomains in protein structure. 1999-2000.
·
PDB - The Protein Data Bank. 1998-2000.
·
QuickPDB - Sequence/structure applet.
1996-1998.
·
MOOSE -
Macromolecular Object Oriented Search Engine 1995-1996.
·
WPDB - MS-Windows macromolecular structure
interrogation 1993-1995.
·
MMQL - Object oriented data model and query
language for macromolecules. 1992-1994.
·
Analysis of
k-tuple clasterization in sequence combinatorial space. 1993-1994.
·
Prediction of
spatially close positions in protein structure on the base of correlated
mutation analysis for homologous protein families. 1991.
·
Multiple
alignment on the base of statistical analysis of diagonal fragments, tree
reconstruction and matrix (profile) representation. 1990-1992.
·
Prediction of
evolutionary mode (adaptive/neutral) on the base of synonymous/nonsynonymous
mutations distribution analysis. 1987-1990.
·
Expert system
for the prediction of protein alpha/beta-domains topology on the base of amino
acid properties, interval scaling and spectral transforms. 1987-1989.
·
Computer
simulation and analysis of regulatory contours with feedbacks evolution.
Application to the molecular evolution interpretation. 1987.
·
Method for
estimation of evolutionary dynamic of variable positions on the base of
homologous sequence data. Model of variable positions dynamic under the protein
structure stability constraints. 1984-1987.
·
Prediction of
protein alpha/beta-domains topology on the base of combinatorial algorithm.
1982-1985.
·
Prediction of
protein structure stability changes under point mutations in human
alpha/beta-hemoglobin on the base of discriminant analysis of amino acid
properties and mutant hemoglobins database. 1982-1985.
SELECTED PUBLICATIONS:
Guda C, Pal
LR, Shindyalov IN. DMAPS: a database of multiple alignments for protein
structures. Nucleic Acids Res, 2006,
34, D273-276.
Ponomarenko J.V., Bourne P.E., Shindyalov I.N.
Assigning new GO annotations to Protein Data Bank sequences by structural
homology. Proteins: Structure, Function
and Bioinformatics, 2005, 58, 855-865.
Li W.W., Byrnes R.W., Hayes J.,
Birnbaum A., Reyes V.M., Shahab A., Mosley C., Pekurovsky D., Quinn G.B., Shindyalov
I.N., Casanova H., Ang L., Berman F., Arzberger P.W., Miller M.A., Bourne
P.E. The encyclopedia of life project: grid software and deployment. New Generation Computing, 2004, 22, 127‑136.
Jia Y.,
Dewey G.T., Shindyalov I.N., Bourne P.E. A new scoring function
and associated statistical significance for structure alignment by CE. J. Comp. Biol., 2004, 11, 787-799.
Guda C., Lu S., Scheeff E.D., Bourne P.E., Shindyalov
I.N. CE-MC: A multiple protein structure alignment server. Nucleic Acids Research, 2004, 32,
W100-W103.
Verentik S., Bourne P.E., Alexandrov
N.N., Shindyalov I.N. Towards consistent assignment of structural
domains in proteins. Journal of Molecular
Biology, 2004, 339, 647-678.
Pekurovsky D., Shindyalov I.N.,
Bourne P.E. High throughput
biological data processing on massively parallel computers. a case study of
pairwise structure comparison and alignment using the combinatorial extension (CE)
algorithm. Bioinformatics, 2004, 20, 1940-1947.
Li W.W., Quinn G.B., Alexandrov N.N.,
Bourne P.E., Shindyalov I.N.
Proteins of Arabidopsis thaliana
(PAT) database: a resource for comparative proteomics. Genome Biology, 2003,
4, R51.
Alexandrov N., Shindyalov
I. PDP: protein domain parser, Bioinformatics,
2003, 19, 429-430.
Ponomarenko J.V., Bourne P.E.,
Solovyev V.V., Shindyalov I.N.
Properties and prediction of protein secondary structure. In:"Current
Topics in Computational Biology", MIT Press, (Jiang T., Xu Y., Zhang M.Q.
eds), 2002, MIT Press, 365-401.
Li W.W., Reddy B.V.B., Shindyalov I.N.,
Bourne P.E. CKAAPs DB: a conserved key amino acid positions database. Nucleic
Acid Research, 2001, 29, 329-331.
Shindyalov I.N., Bourne P.E. CE: A database and tools for 3-D
protein structure comparison and alignment using the Combinatorial Extension
(CE) algorithm. Nucleic Acid Research, 2001, 29, 228-229.
Guda C., Scheeff E.D., Bourne P.E., Shindyalov
I.N. A new algorithm for the alignment of multiple protein structures using
Reddy B.V.B., Li W.W., Shindyalov I.N.,
Bourne P.E. Conserved key amino acid positions (CKAAPs) derived from the
analysis of common substructures in proteins. Proteins: Structure, Function
and Genetics, 2001, 42, 148-163.
Shindyalov I.N., Bourne P.E. An alternative view of protein fold
space. Proteins: Structure, Function and Genetics, 2000, 38, 247-260.
Berman H.M., Westbrook J., Feng Z.,
Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The
Protein Data Bank. Nucleic Acid Research, 2000, 28, 235-242.
Tsigelny I., Shindyalov I.N.,
Bourne P.E., Sudhof T., Taylor P. Common EF-hand motifs in cholinesterases and
neuroligins suggest a role for CA2+ binding in cell surface associations. Protein
Science, 2000, 9, 180-185.
Weissig H., Shindyalov I.N.,
Bourne P.E. Macromolecular structure databases: past progress and future
challenges. Acta Cryst., 1998, D54, 1085-1094.
Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental
combinatorial extension (CE) of the optimal path. Protein Engng, 1998,
9, 739-747.
Shindyalov I.N., Bourne P.E. WPDB - PC Windows-based interrogation
of macromolecular structure. J. Appl. Crystallogr., 1995, 28, 847-852.
Shindyalov I.N., Bourne P.E. Protein data representation and query
using optimized data decomposition. Comput. Applic. Biosci., 1997, 13,
487-496.
Smith C., Gribskov M., Shindyalov I.N.,
Taylor S.S., Ten Eyck L., Veretnik S., Bourne P.E.. The Protein Kinase
Resource, TIBS, 1997, 22, 444-446.
Shindyalov I.N., Kolchanov N.A., Sander C. Can three-dimensional
contacts in protein structures be predicted by analysis of correlated
mutations? Prot. Engng., 1994, 7, 349-358.
Chang W., Shindyalov I.N., Pu C.,
Bourne P.E. Design and application of PDBlib, a C++ macromolecular class
library. Comput. Applic. Biosci., 1994, 10, 575-586.
Shindyalov I.N., Chang W., Pu C., Bourne P.E. MMQL an object
oriented macromolecular query language: prototype data model and
implementation. Prot. Engng., 1994, 7, 1311-1322.
Strelets V.B, Shindyalov I.N., Lim
H.A. Analysis of peptides from known proteins: clusterization in sequence
space. J. Mol. Evol., 1994, 39, 625-630
Shindyalov I.N., Streletc V.B., Kolchanov N.A., Lim H.A. A method
for multiple alignment and its application in homolog compilation. Protein
Seq. Data. Anal., 1993, 4, 219-225.
Shindyalov I.N., Kolchanov N.A. A computer system for the analysis
of molecular evolution in isofunctional gene families. Int. J. Genome
Research, 1993, 1, 129-148.
Kunisawa T., Streletc V., Shindyalov
I.N., Kolchanov N.A. Amplification of genes coding for sensor and
responce-regulator proteins within the Escherichia coli genome. Protein Seq.
Data. Anal., 1993, 5, 237-245.
Streletc V.B., Shindyalov I.N.,
Kolchanov N.A., Milanesi L. Fast, statistically based alignment of amino acid
sequences on the base of diagonal fragments of DOT-matrices. Comput. Applic.
Biosci., 1992, 8, 529-534.
Shindyalov I.N., Bourne P.E. The shape of database to come. DEC
Professional, 1992, 11, 38-44.
Ponomarenko M.P., Benjukh D.N., Salamov
A.A., Solovyev V.V., Shindyalov I.N., Streletz V.B., Orlov Yu. L.,
Kolchanov N.A. Computer system of protein structure and function predictions.
In: "Modelling and Computer Methods in Molecular Biology and
Genetics", ed. V.A. Ratner and N.A. Kolchanov, Nova Science Publishers
Inc.,
Kolchanov N.A., Shindyalov I.N. A
theoretical investigation of evolution of regulatory contours under different
types of selection. In: Problems of Genetics and Theory of Evolution (Shumny
V.K. and Ruvinsky A.O., eds.) Nauka,
Kolchanov N.A., Shindyalov I.N.
Single amino acid substitutions producing instability of globular proteins.
Calculation of their frequencies in the entire mutational spectra of the alpha-
and beta-subunits of human hemoglobin. J. Mol. Evol., 1988, 27, 154-162.
Ponomarenko M.P., Shindyalov I.N.,
Kolchanov N.A. Expert system for prediction topological structure of domains of
globular proteins on the basis of amino acid sequence. Institute of Cytology
and Genetics
Kolchanov N.A., Solovyev V.V., Shindyalov
I.N., Streletz V.B. Application of Computers in Molecular Biology. Structural
Organization of Globular Proteins.
Shindyalov I.N., Kolchanov N.A. Analysis of the factors and
implications of an empirical method for estimating the stability of mutant
human haemoglobins. J. theor. Biol., 1985, 117, 19-46.