E-MSD: an integrated data resource for bioinformatics

A Golovin; T J Oldfield; J G Tate; S Velankar; G J Barton; H Boutselakis; D Dimitropoulos; J Fillon; J M C Ionides; M John; P A Keller; E Krissinel; P McNeil; A Naim; R Newman; A Pajon; J Pineda; A Rachedi; J Copeland; A Sitnov; S Sobhany; A Suarez-Uruena; G J Swaminathan; M Tagari; S Tromm; W Vranken; K Henrick

doi:10.1093/nar/gkh078

E-MSD: an integrated data resource for bioinformatics

A Golovin, T J Oldfield, J G Tate, S Velankar, G J Barton, H Boutselakis, D Dimitropoulos, J Fillon, J M C Ionides, M John, P A Keller, E Krissinel, P McNeil, A Naim, R Newman, A Pajon, J Pineda, A Rachedi, J Copeland, A SitnovS Sobhany, A Suarez-Uruena, G J Swaminathan, M Tagari, S Tromm, W Vranken, K Henrick

Research output: Contribution to journal › Article › peer-review

72 Citations (Scopus)

Abstract

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

Original language	English
Pages (from-to)	D211-6
Journal	Nucleic Acids Research
Volume	32
Issue number	Database issue
DOIs	https://doi.org/10.1093/nar/gkh078
Publication status	Published - 1 Jan 2004

Keywords

Algorithms
Animals
Computational Biology
Databases, Protein
Humans
Internet
Ligands
Proteins
User-Computer Interface

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10.1093/nar/gkh078

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Golovin, A., Oldfield, T. J., Tate, J. G., Velankar, S., Barton, G. J., Boutselakis, H., Dimitropoulos, D., Fillon, J., Ionides, J. M. C., John, M., Keller, P. A., Krissinel, E., McNeil, P., Naim, A., Newman, R., Pajon, A., Pineda, J., Rachedi, A., Copeland, J., ... Henrick, K. (2004). E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Research, 32(Database issue), D211-6. https://doi.org/10.1093/nar/gkh078

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abstract = "The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).",

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Golovin, A, Oldfield, TJ, Tate, JG, Velankar, S, Barton, GJ, Boutselakis, H, Dimitropoulos, D, Fillon, J, Ionides, JMC, John, M, Keller, PA, Krissinel, E, McNeil, P, Naim, A, Newman, R, Pajon, A, Pineda, J, Rachedi, A, Copeland, J, Sitnov, A, Sobhany, S, Suarez-Uruena, A, Swaminathan, GJ, Tagari, M, Tromm, S, Vranken, W & Henrick, K 2004, 'E-MSD: an integrated data resource for bioinformatics', Nucleic Acids Research, vol. 32, no. Database issue, pp. D211-6. https://doi.org/10.1093/nar/gkh078

TY - JOUR

T1 - E-MSD

T2 - an integrated data resource for bioinformatics

AU - Golovin, A

AU - Oldfield, T J

AU - Tate, J G

AU - Velankar, S

AU - Barton, G J

AU - Boutselakis, H

AU - Dimitropoulos, D

AU - Fillon, J

AU - Ionides, J M C

AU - John, M

AU - Keller, P A

AU - Krissinel, E

AU - McNeil, P

AU - Naim, A

AU - Newman, R

AU - Pajon, A

AU - Pineda, J

AU - Rachedi, A

AU - Copeland, J

AU - Sitnov, A

AU - Sobhany, S

AU - Suarez-Uruena, A

AU - Swaminathan, G J

AU - Tagari, M

AU - Tromm, S

AU - Vranken, W

AU - Henrick, K

PY - 2004/1/1

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N2 - The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

AB - The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

KW - Algorithms

KW - Animals

KW - Computational Biology

KW - Databases, Protein

KW - Humans

KW - Internet

KW - Ligands

KW - Proteins

KW - User-Computer Interface

U2 - 10.1093/nar/gkh078

DO - 10.1093/nar/gkh078

M3 - Article

C2 - 14681397

SN - 0305-1048

VL - 32

SP - D211-6

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

E-MSD: an integrated data resource for bioinformatics

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Keywords

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