Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules

Israel Gelland; Alexander Kister; Casimir Kulikowski; Ognyan Stoyanov

Algorithmic determination of core positions in the V_L and V_H domains of immunoglobulin molecules

Israel Gelland, Alexander Kister, Casimir Kulikowski, Ognyan Stoyanov

School of Arts and Sciences, Computer Science

Rutgers, The State University

Research output: Contribution to conference › Paper › peer-review

Abstract

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_α(I)-C_α(J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units - strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures lead to the identification of two geometrical core sets of C_α atom positions for the V_L and V_H domains. Applications of the core sets are described.

Original language	American English
Pages	85-93
Number of pages	9
State	Published - 1998
Event	Proceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology - New York, NY, USA Duration: Mar 22 1998 → Mar 25 1998

Other

Other	Proceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology
City	New York, NY, USA
Period	3/22/98 → 3/25/98

ASJC Scopus subject areas

General Computer Science
General Biochemistry, Genetics and Molecular Biology

Cite this

@conference{a1dd070cc69e463d9b53d2f980bd6f3d,

title = "Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules",

abstract = "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 Cα(I)-Cα(J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units - strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures lead to the identification of two geometrical core sets of Cα atom positions for the VL and VH domains. Applications of the core sets are described.",

author = "Israel Gelland and Alexander Kister and Casimir Kulikowski and Ognyan Stoyanov",

year = "1998",

language = "American English",

pages = "85--93",

note = "Proceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology ; Conference date: 22-03-1998 Through 25-03-1998",

}

Algorithmic determination of core positions in the V_L and V_H domains of immunoglobulin molecules. / Gelland, Israel; Kister, Alexander; Kulikowski, Casimir et al.
1998. 85-93 Paper presented at Proceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology, New York, NY, USA.

Research output: Contribution to conference › Paper › peer-review

TY - CONF

T1 - Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules

AU - Gelland, Israel

AU - Kister, Alexander

AU - Kulikowski, Casimir

AU - Stoyanov, Ognyan

PY - 1998

Y1 - 1998

N2 - 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 Cα(I)-Cα(J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units - strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures lead to the identification of two geometrical core sets of Cα atom positions for the VL and VH domains. Applications of the core sets are described.

AB - 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 Cα(I)-Cα(J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units - strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures lead to the identification of two geometrical core sets of Cα atom positions for the VL and VH domains. Applications of the core sets are described.

UR - http://www.scopus.com/inward/record.url?scp=0031655866&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0031655866&partnerID=8YFLogxK

M3 - Paper

SP - 85

EP - 93

T2 - Proceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology

Y2 - 22 March 1998 through 25 March 1998

ER -

Algorithmic determination of core positions in the V_L and V_H domains of immunoglobulin molecules

Abstract

Other

ASJC Scopus subject areas

Other files and links

Fingerprint

Cite this