Search Results - "Shindyalov, Ilya N."

Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology by Ponomarenko, Julia V., Bourne, Philip E., Shindyalov, Ilya N.

“…Accompanying the discovery of an increasing number of proteins, there is the need to provide functional annotation that is both highly accurate and consistent…”
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The Protein Data Bank by Berman, H M, Westbrook, J, Feng, Z, Gilliland, G, Bhat, T N, Weissig, H, Shindyalov, I N, Bourne, P E

“…The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes…”
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Partitioning Protein Structures into Domains: Why Is it so Difficult? by Holland, Timothy A., Veretnik, Stella, Shindyalov, Ilya N., Bourne, Philip E.

“…This analysis takes an in-depth look into the difficulties encountered by automatic methods for domain decomposition from three-dimensional structure. The…”
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Building an automated classification of DNA-binding protein domains by Ponomarenko, Julia V., Bourne, Philip E., Shindyalov, Ilya N.

“…Intensive growth in 3D structure data on DNA-protein complexes as reflected in the Protein Data Bank (PDB) demands new approaches to the annotation and…”
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CE-MC: a multiple protein structure alignment server by Guda, Chittibabu, Lu, Sifang, Scheeff, Eric D., Bourne, Philip E., Shindyalov, Ilya N.

“…CE-MC server (http://cemc.sdsc.edu) provides a web-based facility for the alignment of multiple protein structures based on C-α coordinate distances, using…”
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Toward Consistent Assignment of Structural Domains in Proteins by Veretnik, Stella, Bourne, Philip E, Alexandrov, Nickolai N, Shindyalov, Ilya N

“…The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function, yet little quality…”
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A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm by Shindyalov, Ilya N., Bourne, Philip E.

“…The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list…”
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DMAPS: a database of multiple alignments for protein structures by Guda, Chittibabu, Pal, Lipika R, Shindyalov, Ilya N

“…The database of multiple alignments for protein structures (DMAPS) provides instant access to pre-computed multiple structure alignments for all protein…”
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A comparative proteomics resource: proteins of Arabidopsis thaliana by Li, Wilfred W, Quinn, Greg B, Alexandrov, Nickolai N, Bourne, Philip E, Shindyalov, Ilya N

“…Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, we analyzed all the proteins of…”
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A new scoring function and associated statistical significance for structure alignment by CE by Jia, Yuting, Dewey, T Gregory, Shindyalov, Ilya N, Bourne, Philip E

“…A new scoring function for assessing the statistical significance of protein structure alignment has been developed. The new scores were tested empirically…”
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Structure comparison and alignment by Bourne, Philip E, Shindyalov, Ilya N

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CKAAPs DB: a Conserved Key Amino Acid Positions DataBase by Li, Wilfred W., Reddy, Boojala V. B., Tate, John G., Shindyalov, Ilya N., Bourne, Philip E.

“…The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key…”
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CKAAPs DB: a conserved key amino acid positions database by Li, W W, Reddy, B V, Shindyalov, I N, Bourne, P E

“…The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key…”
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Protein structure alignment by incremental combinatorial extension (CE) of the optimal path by Shindyalov, I N, Bourne, P E

“…A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment…”
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An alternative view of protein fold space by Shindyalov, Ilya N., Bourne, Philip E.

“…Comparing and subsequently classifying protein structures information has received significant attention concurrent with the increase in the number of…”
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The protein kinase resource by Smith, Christopher M., Shindyalov, Ilya N., Veretnik, Stella, Gribskov, Michael, Taylor, Susan S., Ten Eyck, Lynn F., Bourne, Philip E.

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Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins by Reddy, Boojala V.B., Li, Wilfred W., Shindyalov, Ilya N., Bourne, Philip E.

“…An all‐against‐all protein structure comparison using the Combinatorial Extension (CE) algorithm applied to a representative set of PDB structures revealed a…”
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The encyclopedia of life project: Grid software and deployment by Li, Wilfred W., Byrnes, Robert W., Hayes, Jim, Birnbaum, Adam, Reyes, Vicente M., Shahab, Atif, Mosley, Coleman, Pekurovsky, Dmitry, Quinn, Greg B., Shindyalov, Ilya N., Casanova, Henri, Ang, Larry, Berman, Fran, Arzberger, Peter W., Miller, Mark A., Bourne, Philip E.

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Protein data representation and query using optimized data decomposition by Shindyalov, Ilya N., Bourne, Philip E.

“…Motivation: To provide data management tools to maintain and query efficiently experimental and derived protein data with the goal of providing new insights…”
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Analysis of peptides from known proteins: clusterization in sequence space by Strelets, V B, Shindyalov, I N, Lim, H A

“…A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to…”
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