High-throughput computational and experimental techniques in structural genomics

Mark R. Chance, Andras Fiser, Andrej Sali, Ursula Pieper, Narayanan Eswar, Guiping Xu, Jorge E. Fajardo, Thirumuruhan Radhakannan, Nebojsa Marinkovic

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10%-15% of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.

Original languageEnglish (US)
Pages (from-to)2145-2154
Number of pages10
JournalGenome Research
Volume14
Issue number10 B
StatePublished - Oct 2004

Fingerprint

Genomics
Open Reading Frames
Metals
Proteins
Molecular Sequence Annotation
Structural Models
Computational Biology
Organism Cloning
Genome
Databases
Research

ASJC Scopus subject areas

  • Genetics

Cite this

Chance, M. R., Fiser, A., Sali, A., Pieper, U., Eswar, N., Xu, G., ... Marinkovic, N. (2004). High-throughput computational and experimental techniques in structural genomics. Genome Research, 14(10 B), 2145-2154.

High-throughput computational and experimental techniques in structural genomics. / Chance, Mark R.; Fiser, Andras; Sali, Andrej; Pieper, Ursula; Eswar, Narayanan; Xu, Guiping; Fajardo, Jorge E.; Radhakannan, Thirumuruhan; Marinkovic, Nebojsa.

In: Genome Research, Vol. 14, No. 10 B, 10.2004, p. 2145-2154.

Research output: Contribution to journalArticle

Chance, MR, Fiser, A, Sali, A, Pieper, U, Eswar, N, Xu, G, Fajardo, JE, Radhakannan, T & Marinkovic, N 2004, 'High-throughput computational and experimental techniques in structural genomics', Genome Research, vol. 14, no. 10 B, pp. 2145-2154.
Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G et al. High-throughput computational and experimental techniques in structural genomics. Genome Research. 2004 Oct;14(10 B):2145-2154.
Chance, Mark R. ; Fiser, Andras ; Sali, Andrej ; Pieper, Ursula ; Eswar, Narayanan ; Xu, Guiping ; Fajardo, Jorge E. ; Radhakannan, Thirumuruhan ; Marinkovic, Nebojsa. / High-throughput computational and experimental techniques in structural genomics. In: Genome Research. 2004 ; Vol. 14, No. 10 B. pp. 2145-2154.
@article{6a1acc3d8fe94763b14af8002c8572a4,
title = "High-throughput computational and experimental techniques in structural genomics",
abstract = "Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10{\%}-15{\%} of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.",
author = "Chance, {Mark R.} and Andras Fiser and Andrej Sali and Ursula Pieper and Narayanan Eswar and Guiping Xu and Fajardo, {Jorge E.} and Thirumuruhan Radhakannan and Nebojsa Marinkovic",
year = "2004",
month = "10",
language = "English (US)",
volume = "14",
pages = "2145--2154",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "10 B",

}

TY - JOUR

T1 - High-throughput computational and experimental techniques in structural genomics

AU - Chance, Mark R.

AU - Fiser, Andras

AU - Sali, Andrej

AU - Pieper, Ursula

AU - Eswar, Narayanan

AU - Xu, Guiping

AU - Fajardo, Jorge E.

AU - Radhakannan, Thirumuruhan

AU - Marinkovic, Nebojsa

PY - 2004/10

Y1 - 2004/10

N2 - Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10%-15% of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.

AB - Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10%-15% of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.

UR - http://www.scopus.com/inward/record.url?scp=7444267932&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=7444267932&partnerID=8YFLogxK

M3 - Article

C2 - 15489337

AN - SCOPUS:7444267932

VL - 14

SP - 2145

EP - 2154

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 10 B

ER -