25 research outputs found
Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network
Computational identification of heme-binding residues is beneficial for predicting and designing novel heme proteins. Here we proposed a novel method for heme-binding residue prediction by exploiting topological properties of these residues in the residue interaction networks derived from three-dimensional structures. Comprehensive analysis showed that key residues located in heme-binding regions are generally associated with the nodes with higher degree, closeness and betweenness, but lower clustering coefficient in the network. HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features. The results showed that incorporation of network-based features significantly improved the prediction performance. We also compared the residue interaction networks of heme proteins before and after heme binding and found that the topological features can well characterize the heme-binding sites of apo structures as well as those of holo structures, which led to reliable performance improvement as we applied HemeNet to predicting the binding residues of proteins in the heme-free state. HemeNet web server is freely accessible at http://mleg.cse.sc.edu/hemeNet/
Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts
Glutamic acid promotes monacolin K production and monacolin K biosynthetic gene cluster expression in Monascus
Effect of Monascus as a nitrite substitute on color, lipid oxidation, and proteolysis of fermented meat mince
Adolescent cannabinoid exposure induces irritability-like behavior and cocaine cross-sensitization without affecting the escalation of cocaine self-administration in adulthood
Bioproduction of hydrolytic enzymes using apple pomace waste by A. niger: applications in biocontrol formulations and hydrolysis of chitin/chitosan
Amyloid formation under physiological conditions proceeds via a native-like folding intermediate
Conformational Characterization of Intrinsically Disordered Proteins and Its Biological Significance
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