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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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One of the four snapshots displayed in HotSprint generated by Rasmol for interface 1yp2AB. An interface is composed of two sides (chain A and chain B of potato tuber ADP-glucose phyrophosphorylase with PDB ID 1yp2) from two interacting proteins. Interface residues are shown as balls whereas the rest of the protein is shown as the trace. The purple and red residues represent interface residues of the A and B chains of the interface, respectively. The yellow and green residues are predicted hot spots on the chains A and B, respectively.
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Figure 3: One of the four snapshots displayed in HotSprint generated by Rasmol for interface 1yp2AB. An interface is composed of two sides (chain A and chain B of potato tuber ADP-glucose phyrophosphorylase with PDB ID 1yp2) from two interacting proteins. Interface residues are shown as balls whereas the rest of the protein is shown as the trace. The purple and red residues represent interface residues of the A and B chains of the interface, respectively. The yellow and green residues are predicted hot spots on the chains A and B, respectively.

Mentions: The page presenting interface information consists of three main sections. In the first section, overall properties of the interface such as number of computational hot spots on the interface, number of conserved residues on the interface, average conservation score of interface residues and buried ASA of the interface are presented. The next section lists residues of the interface along with their position, name, conservation score, ASA in monomer, ASA in complex, type (contacting interface residue, neighboring interface residue or none). A residue is highlighted with a red background if it is a computational hot spot. Static snapshots of the interface from four different perspectives are shown using Rasmol (26) at the bottom of the page (Figure 3). It is possible to include only contacting residues in the presented results using the check box at the bottom of the query box.Figure 3.


HotSprint: database of computational hot spots in protein interfaces.

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

One of the four snapshots displayed in HotSprint generated by Rasmol for interface 1yp2AB. An interface is composed of two sides (chain A and chain B of potato tuber ADP-glucose phyrophosphorylase with PDB ID 1yp2) from two interacting proteins. Interface residues are shown as balls whereas the rest of the protein is shown as the trace. The purple and red residues represent interface residues of the A and B chains of the interface, respectively. The yellow and green residues are predicted hot spots on the chains A and B, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: One of the four snapshots displayed in HotSprint generated by Rasmol for interface 1yp2AB. An interface is composed of two sides (chain A and chain B of potato tuber ADP-glucose phyrophosphorylase with PDB ID 1yp2) from two interacting proteins. Interface residues are shown as balls whereas the rest of the protein is shown as the trace. The purple and red residues represent interface residues of the A and B chains of the interface, respectively. The yellow and green residues are predicted hot spots on the chains A and B, respectively.
Mentions: The page presenting interface information consists of three main sections. In the first section, overall properties of the interface such as number of computational hot spots on the interface, number of conserved residues on the interface, average conservation score of interface residues and buried ASA of the interface are presented. The next section lists residues of the interface along with their position, name, conservation score, ASA in monomer, ASA in complex, type (contacting interface residue, neighboring interface residue or none). A residue is highlighted with a red background if it is a computational hot spot. Static snapshots of the interface from four different perspectives are shown using Rasmol (26) at the bottom of the page (Figure 3). It is possible to include only contacting residues in the presented results using the check box at the bottom of the query box.Figure 3.

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