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HotSprint: database of computational hot spots in protein interfaces.

Guney E, Tuncbag N, Keskin O, Gursoy A - Nucleic Acids Res. (2007)

Bottom Line: HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006.Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others.A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces.

View Article: PubMed Central - PubMed

Affiliation: Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

ABSTRACT
We present a new database of computational hot spots in protein interfaces: HotSprint. Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006. The conserved residues in interfaces with certain buried accessible solvent area (ASA) and complex ASA thresholds are flagged as computational hot spots. The predicted hot spots are observed to correlate with the experimental hot spots with an accuracy of 76%. Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others. A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces. HotSprint is available at http://prism.ccbb.ku.edu.tr/hotsprint; and it provides information for interface residues that are functionally and structurally important as well as the evolutionary history and solvent accessibility of residues in interfaces.

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Related in: MedlinePlus

Interface information page for 1yp2AB Interface. Overall properties (number of computational hot spots, number of conserved residues, average conservation score, buried ASA and a link to interface information in the original dataset), individual residues and graphical representation of the interface are all displayed in this page. Using the link to the original dataset, users can get detailed information about interfaces: whether it is a biological or crystal interface, and interface amino acid composition. The graphical representation part contains snapshots of the interface and its hot spots from four different perspectives and a Jmol plugin is loaded in a new window when these images are clicked.
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Figure 2: Interface information page for 1yp2AB Interface. Overall properties (number of computational hot spots, number of conserved residues, average conservation score, buried ASA and a link to interface information in the original dataset), individual residues and graphical representation of the interface are all displayed in this page. Using the link to the original dataset, users can get detailed information about interfaces: whether it is a biological or crystal interface, and interface amino acid composition. The graphical representation part contains snapshots of the interface and its hot spots from four different perspectives and a Jmol plugin is loaded in a new window when these images are clicked.

Mentions: The first query box allows the user to fetch associated interfaces of a given protein using its PDB identifier. The default thresholds in these expressions can also be modified by the user. If there exists only a single interface associated with the input PDB identifier (e.g. for PDB ID: 1axd), then information for that interface (1axdAB) is displayed. However, there may be more than one interface extracted from that protein. In this case, interface identifiers of interfaces associated with that PDB are displayed (e.g. for the PDB ID 1yp2, four interfaces are available 1yp2AB, 1yp2AD, 1yp2BC and 1yp2CD). When one selects one of the interface identifiers listed, information for that interface is presented. Figure 2 demonstrates the result page yielded after querying the interface 1yp2AB among the associated interfaces of 1yp2.Figure 2.


HotSprint: database of computational hot spots in protein interfaces.

Guney E, Tuncbag N, Keskin O, Gursoy A - Nucleic Acids Res. (2007)

Interface information page for 1yp2AB Interface. Overall properties (number of computational hot spots, number of conserved residues, average conservation score, buried ASA and a link to interface information in the original dataset), individual residues and graphical representation of the interface are all displayed in this page. Using the link to the original dataset, users can get detailed information about interfaces: whether it is a biological or crystal interface, and interface amino acid composition. The graphical representation part contains snapshots of the interface and its hot spots from four different perspectives and a Jmol plugin is loaded in a new window when these images are clicked.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238999&req=5

Figure 2: Interface information page for 1yp2AB Interface. Overall properties (number of computational hot spots, number of conserved residues, average conservation score, buried ASA and a link to interface information in the original dataset), individual residues and graphical representation of the interface are all displayed in this page. Using the link to the original dataset, users can get detailed information about interfaces: whether it is a biological or crystal interface, and interface amino acid composition. The graphical representation part contains snapshots of the interface and its hot spots from four different perspectives and a Jmol plugin is loaded in a new window when these images are clicked.
Mentions: The first query box allows the user to fetch associated interfaces of a given protein using its PDB identifier. The default thresholds in these expressions can also be modified by the user. If there exists only a single interface associated with the input PDB identifier (e.g. for PDB ID: 1axd), then information for that interface (1axdAB) is displayed. However, there may be more than one interface extracted from that protein. In this case, interface identifiers of interfaces associated with that PDB are displayed (e.g. for the PDB ID 1yp2, four interfaces are available 1yp2AB, 1yp2AD, 1yp2BC and 1yp2CD). When one selects one of the interface identifiers listed, information for that interface is presented. Figure 2 demonstrates the result page yielded after querying the interface 1yp2AB among the associated interfaces of 1yp2.Figure 2.

Bottom Line: HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006.Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others.A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces.

View Article: PubMed Central - PubMed

Affiliation: Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

ABSTRACT
We present a new database of computational hot spots in protein interfaces: HotSprint. Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006. The conserved residues in interfaces with certain buried accessible solvent area (ASA) and complex ASA thresholds are flagged as computational hot spots. The predicted hot spots are observed to correlate with the experimental hot spots with an accuracy of 76%. Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others. A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces. HotSprint is available at http://prism.ccbb.ku.edu.tr/hotsprint; and it provides information for interface residues that are functionally and structurally important as well as the evolutionary history and solvent accessibility of residues in interfaces.

Show MeSH
Related in: MedlinePlus