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3.1 Papers
Section Intro | Molecular modeling | Bioinformatics | docking | Methods and algorithms | Applications | Chronological list

3.1.6 Chronological list
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3.1.6.32 Totrov, M.M., and Abagyan, R.A. (1994). Detailed ab initio prediction of lysozyme-antibody complex with 1.6 accuracy. Nature Structural Biology, 1, 259-263

The fundamental event in biological assembly is association of two biological macromolecules. Here we present a successful, accurate ab initio prediction of the binding of uncomplexed lysozyme to the HyHel5 antibody. The prediction combines pseudo Brownian Monte Carlo minimization with a biased-probability global side-chain placement procedure. It was effected in an all-atom representation, with ECEPP/2 potentials complemented with the surface energy, side-chain entropy and electrostatic polarization free energy. The near-native solution found was surprisingly close to the crystallographic structure (root-mean-square deviation of 1.57 A for all backbone atoms of lysozyme) and had a considerably lower energy (by 20 kcal/mol) than any other solution.