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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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View of numb protein phosphotyrosine binding (PTB) domain. Red and yellow residues are experimental hot spots. Red residues are correctly predicted by HotSprint. Left and right figures present the results for the prediction of hot spots using pScore and pScore + ASA, respectively. VMD (29) is used to graphically represent the protein.
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Figure 4: View of numb protein phosphotyrosine binding (PTB) domain. Red and yellow residues are experimental hot spots. Red residues are correctly predicted by HotSprint. Left and right figures present the results for the prediction of hot spots using pScore and pScore + ASA, respectively. VMD (29) is used to graphically represent the protein.

Mentions: As a case study, we compare the experimental hot spots of the numb PTB domain with HotSprint predictions. Figure 4 displays the ribbon diagram of the numb PTB domain that is in complex with numb-associated kinase (NAK)-C (PDB ID: 1ddm) (27). Numb PTB domain is known to interact with a diverse set of peptides through a large hydrophobic cavity on its surface (28). The left figure presents the predicted hot spots by using pScore only, whereas the right panel illustrates the results when the pScore + ASA is used. Red and yellow residues are the identified as hot spots by alanine scanning substitutions on the protein complex. Considering only propensity scaled conservation scores of the residues (left figure) in the interface of 1ddmAB, 8 of the 10 experimentally identified hot spots (red residues) are predicted computationally. Including ASA further filters some of the hot spot predictions (5 of the 10 hot spots are predicted).Figure 4.


HotSprint: database of computational hot spots in protein interfaces.

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

View of numb protein phosphotyrosine binding (PTB) domain. Red and yellow residues are experimental hot spots. Red residues are correctly predicted by HotSprint. Left and right figures present the results for the prediction of hot spots using pScore and pScore + ASA, respectively. VMD (29) is used to graphically represent the protein.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: View of numb protein phosphotyrosine binding (PTB) domain. Red and yellow residues are experimental hot spots. Red residues are correctly predicted by HotSprint. Left and right figures present the results for the prediction of hot spots using pScore and pScore + ASA, respectively. VMD (29) is used to graphically represent the protein.
Mentions: As a case study, we compare the experimental hot spots of the numb PTB domain with HotSprint predictions. Figure 4 displays the ribbon diagram of the numb PTB domain that is in complex with numb-associated kinase (NAK)-C (PDB ID: 1ddm) (27). Numb PTB domain is known to interact with a diverse set of peptides through a large hydrophobic cavity on its surface (28). The left figure presents the predicted hot spots by using pScore only, whereas the right panel illustrates the results when the pScore + ASA is used. Red and yellow residues are the identified as hot spots by alanine scanning substitutions on the protein complex. Considering only propensity scaled conservation scores of the residues (left figure) in the interface of 1ddmAB, 8 of the 10 experimentally identified hot spots (red residues) are predicted computationally. Including ASA further filters some of the hot spot predictions (5 of the 10 hot spots are predicted).Figure 4.

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