STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces

Abstract

http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).

A Single Amino Acid Difference within the α-2 Domain of Two Naturally Occurring Equine MHC Class I Molecules Alters the Recognition of Gag and Rev Epitopes by Equine Infectious Anemia Virus-Specific CTL

“…To model the binding of the three peptides to 7-6 and 141, the docking program FTDock2.0 (ͳwww.bmm.icnet.uk/dockingʹ) (74 -76) was used, and the docking score (RPScore) for each complex was determined (76). The interacting residues for each complex were identified, and the interactions by category (hydrophobic, salt bridges, repulsive charged, hydrogen bonds, and aromatic stacking) between atoms of contact residues were determined using the STING Millennium Suite program (ͳhttp://trantor.bioc.columbia.edu/SMS/index_m.htmlʹ) (77,78). Finally, the models were visualized using the PyMOL Molecular Graphics System (DeLano Scientific, ͳwww.pymol.orgʹ).…”

Assessing methods for identifying pair-wise atomic contacts across binding interfaces

“…Instead, this method uses Chothia (1974) radii set to calculate the vdW radii. If two atoms were found to be within the sum of their water probe, then they were considered to be in contact (Lo Conte et al, 1999;Mancini et al, 2004).…”

“…Those residues that exhibit a change in SASA between the two states are considered to be involved in the interaction. Any SASA changes in the complex compared to the monomers are examined to see what neighboring atoms are within the SASA probe plus vdW radii distance (Mancini et al, 2004;Sobolev et al, 1999). There are two main drawbacks in the DSASA method: the surface area of an interface is overestimated (McConkey et al, 2002;Sobolev et al, 1999) and in many cases the implementation does not adequately identify pair-wise contacts.…”

Induction of Neutralizing Antibodies against Mutalysin-II from Lachesis muta muta Snake Venom Elicited by a Conformational B-cell Epitope Predicted by Blue Star Sting Data Base

“…Prediction of the epitopes by selecting amino acid residues with specific physical-chemical and structural attributes available in Blue Star Sting database Due to the rich repository of protein characteristics offered by BlueStar STING (BSS) platform [16][17][18][19], which is the latest version of SMS, has already been used to predict enzyme class [20], proteinligand analysis [21,22], protein mutant analysis [23,24], protein-protein interaction pattern analysis [25] and others [26,27]. In this work, BSS platform was used as a tool to predict a conformational epitope of Mut-II based on its physicochemical properties.…”