Abstract
An efficient 'soft docking' algorithm is described to assist the prediction of protein-protein association using three-dimensional structures of molecules. The basic tools are the 'simplified protein' model and the docking algorithm of Wodak and Janin. The side chain flexibility of Arg, Lys, Asp, Glu and Met residues at the protein surface is taken into account. The complex type-dependent filtering technique on the basis of the geometric matching, hydrophobicity and electrostatic complementarity is used to select candidate binding modes. Subsequently, we calculate a scoring function which includes electrostatic and desolvation energy terms. In the 44 complexes tested including enzyme-inhibitor, antibody-antigen and other complexes, native-like structures were all found, of which 30 were ranked in the top 20. Thus, our soft docking algorithm has the potential to predict protein-protein recognition.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
