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Structural determinants in the sequences of immunoglobulin variable domain.
Chothia C, Gelfand I, Kister A. Chothia C, et al. J Mol Biol. 1998 May 1;278(2):457-79. doi: 10.1006/jmbi.1998.1653. J Mol Biol. 1998. PMID: 9571064
Comparison of the different known structures shows that they have a core of 76 residues which has the same main-chain conformation in all structures. ...The regions that differ in conformation are the three hypervariable regions, three other inter-strand turns and a
Comparison of the different known structures shows that they have a core of 76 residues which has the same main-chain conformation in …
Geometric invariant core for the CL and CH1 domains of immunoglobulin molecules.
Stoyanov O, Kister A, Gelfand I, Kulikowski C, Chothia C. Stoyanov O, et al. J Comput Biol. 2000;7(5):673-84. doi: 10.1089/106652701446143. J Comput Biol. 2000. PMID: 11153093
A previously developed algorithmic method for identifying a geometric invariant of protein structures, termed geometrical core, is extended to the C(L) and C(H1) domains of immunoglobulin molecules. ...
A previously developed algorithmic method for identifying a geometric invariant of protein structures, termed geometrical core
Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules.
Gelfand I, Kister A, Kulikowski C, Stoyanov O. Gelfand I, et al. J Comput Biol. 1998 Fall;5(3):467-77. doi: 10.1089/cmb.1998.5.467. J Comput Biol. 1998. PMID: 9773343
We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the C alpha (I) - C alpha (J) atom distances are identi …
We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition …
Protein--protein recognition: juxtaposition of domain and interface cores in immunoglobulins and other sandwich-like proteins.
Potapov V, Sobolev V, Edelman M, Kister A, Gelfand I. Potapov V, et al. J Mol Biol. 2004 Sep 10;342(2):665-79. doi: 10.1016/j.jmb.2004.06.072. J Mol Biol. 2004. PMID: 15327963
Structural analysis of a non-redundant data set of 47 immunoglobulin (Ig) proteins was carried out using a combination of criteria: atom--atom contact compatibility, position occupancy rate, conservation of residue type and positional conservation in 3D space. ...Th …
Structural analysis of a non-redundant data set of 47 immunoglobulin (Ig) proteins was carried out using a combination of crit …
Predicting amino acid sequences of the antibody human VH chains from its first several residues.
Galitsky BA, Gelfand IM, Kister AE. Galitsky BA, et al. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5193-8. doi: 10.1073/pnas.95.9.5193. Proc Natl Acad Sci U S A. 1998. PMID: 9560252 Free PMC article.
A new method for classification of Ig sequences is suggested. The defining characteristic of a class is presence of particular residues at several class-determining positions. ...We developed a software tool for analysis, classification, and prediction of res
A new method for classification of Ig sequences is suggested. The defining characteristic of a class is presence of particular
A very limited number of keywords (main patterns) describes all sequences of the human variable heavy (VH) and kappa (Vkappa) domains.
Gelfand IM, Kister AE. Gelfand IM, et al. Proc Natl Acad Sci U S A. 1997 Nov 11;94(23):12562-7. doi: 10.1073/pnas.94.23.12562. Proc Natl Acad Sci U S A. 1997. PMID: 9356489 Free PMC article.
Thus, knowing the keywords, one can determine whether any given small part of a sequence belongs to a heavy or kappa chain and predict its precise localization in the sequence. ...
Thus, knowing the keywords, one can determine whether any given small part of a sequence belongs to a heavy or kappa chain and …
Prediction of the structural motifs of sandwich proteins.
Fokas AS, Gelfand IM, Kister AE. Fokas AS, et al. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16780-3. doi: 10.1073/pnas.0407570101. Epub 2004 Nov 18. Proc Natl Acad Sci U S A. 2004. PMID: 15550537 Free PMC article.
We investigate the supersecondary structure of a large group of proteins, the so-called sandwich proteins. The analysis of a large number of such proteins has led us to propose a set of rules that can be used to predict the possible arrangements of strands in …
We investigate the supersecondary structure of a large group of proteins, the so-called sandwich proteins. The analysis of a l …
Common features in structures and sequences of sandwich-like proteins.
Kister AE, Finkelstein AV, Gelfand IM. Kister AE, et al. Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14137-41. doi: 10.1073/pnas.212511499. Epub 2002 Oct 16. Proc Natl Acad Sci U S A. 2002. PMID: 12384574 Free PMC article.
As homology among these proteins is not usually detectable even with the most powerful sequence-comparing algorithms, we employed a structure-based approach to sequence alignment. ...A residue at any of these positions possesses similar structural properties with re …
As homology among these proteins is not usually detectable even with the most powerful sequence-comparing algorithms, we employed a s …
Class-defining characteristics in the mouse heavy chains of variable domains.
Galitsky BA, Gelfand IM, Kister AE. Galitsky BA, et al. Protein Eng. 1999 Nov;12(11):919-25. doi: 10.1093/protein/12.11.919. Protein Eng. 1999. PMID: 10585497
Because a strong correlation of residues was found, one only needs several residues to classify a sequence. It follows that no all residue alignment procedure is necessary to divide sequences into classes. An important corollary of our approach is the possibility of …
Because a strong correlation of residues was found, one only needs several residues to classify a sequence. It follows that no …
A geometric construction determines all permissible strand arrangements of sandwich proteins.
Fokas AS, Papatheodorou TS, Kister AE, Gelfand IM. Fokas AS, et al. Among authors: kister ae. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15851-3. doi: 10.1073/pnas.0507335102. Epub 2005 Oct 25. Proc Natl Acad Sci U S A. 2005. PMID: 16249331 Free PMC article.
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