geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

HotSprint: database of computational hot spots in protein interfaces


, : HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Research 36(Database Issue): D662-D666

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.

US$19.90

PMID: 17959648

DOI: 10.1093/nar/gkm813


Other references

Fast T.; Kliest J.; Boleij J.S.M.; Slingerland P., 1988: The influence of soil pollution on the indoor air quality. Wolf, K , W J Van Den Brink And F J Colon (Ed ) Contaminated Soil '88; Second International Netherlands Organization For Applied Scientific Research/Federal Ministry Of Research And Technology Conference, Hamburg, West Germany, April 11-15, Xxxvi+1009p (Vol 1); Xxv+683p (Vol 2) Kluwer Academic Publishers: Dordrecht, Netherlands; Boston, Massachusetts, Usa Illus Maps 441-450

Liem, T.K.; Krishnamoorthy, M.; Applebaum, H.; Kolata, R.; Rudd, R.G.; Chen, W., 1996: A comparison of the hemodynamic and ventilatory effects of abdominal insufflation with helium and carbon dioxide in young swine. Abdominal CO2 insufflation has been shown to cause hypercarbia, acidemia, and decreased oxygenation in a pediatric animal model. Such metabolic derangements have prompted a search for alternative insufflation gases. This study compares the hemodyn...

Papiernik, E.; Bucourt, M.; Zeitlin, J.; Senanedj, P.; Topuz, B., 2001: Regionalization of perinatal care in the Seine-Saint-Denis department of France. To evaluate a policy designed to regionalize perinatal care in the Seine-Saint-Denis department of France. The place of birth of every preterm infant (born before 33 weeks gestation) in 1998-1999 was compared with that for the period of 1989-1992....

Okada, K.; Yagi, A.; Tamio, T.; Sakuramoto, K.; Saigusa, T.; Okajima, K.; Yonemitsu, A.; Siraki, M., 1981: Diagnostic evaluation of CT and ERCP based on a retrospective analysis of hepato-biliary and pancreatic diseases. A retrospective analysis was performed in order to evaluate diagnostic accuracies by computed tomography (CT) and by endoscopic retrograde cholangiopancreatography (ERCP). Materials studied were 67 lesions out of 56 cases with hepato-biliary and p...

Fernandes, G., 1968: Some aspects of care and management of inbred strains of mice. Indian Journal of Medical Sciences 22(5): 315-328

Alexander, D.M., 1911: The Use of Leucocytic Extract in Infective Processes. British Medical Journal 1(2616): 355-357

Towl, G., 2012: Editorial. The importance of an evidence-based approach. Evidence-Based Mental Health 15(1): 1-1

Shikata H.; Utsumi N.; Fujimoto D., 1987: Collagen in aging bone of the jaw. Ferguson, D B (Ed ) Frontiers Of Oral Physiology, Vol 6 The Aging Mouth Viii+175p S Karger Ag: Basel, Switzerland; New York, New York, Usa Illus 85-95

Verkhusha, V.V.; Akovbian, N.A.; Efremenko, E.N.; Varfolomeyev, S.D.; Vrzheshch, P.V., 2002: Kinetic analysis of maturation and denaturation of DsRed, a coral-derived red fluorescent protein. The red fluorescent protein DsRed recently cloned from Discosoma coral, with its significantly red-shifted excitation and emission maxima (558 and 583 nm, respectively), has attracted great interest because of its spectral complementation to other...

Mindello Neto, U.R., 2006: Hardwood cuttings rooting of plum tree cultivars with application of indolbutyric acid and hydrogen cyanamide. The effects of indole-butyric acid (IBA; 0 or 4000 mg/litre) and hydrogen cyanamide (0.0, 0.5 or 1.0%) on the rooting of hardwood cuttings of 3 cultivars of plum tree (Pluma 7, Rosa Mineira and Amarelinha) were studied under greenhouse conditions....