… based on the physical contributions to the interaction, and should therefore be more universal
and transferable than knowledge-based … evaluating the electrostatic free energy of just one …

… Thus by calculating the contribution of a mutation to the electrostatic energy of interaction,
we can predict the degree to which this change will increase or decrease the rate of …

… the ligand—macromolecule interaction energy that show good predictive … interaction energies
of parts of the ligands and key regions of the macromolecule. Application to the interaction …

… Our implementation of the above approach, which we will refer to as the linear interaction
energy (LIE) approximation, is based on evaluation of ligand interaction energetics in the …

… experimentally, the determination of the interaction energies of these complexes which are
… interactions is on how an interplay of attractive and repulsive forces govern the interaction of …

… The only term representing polar interactions in this scoring function is a simple hydrogen …
In conclusion, the standard parametrization of eq 1 can predict the binding free energies of the …

… to predict, from the amino acid sequence, lowest energy conformations … interactions, we
test it on short peptides and protein segments that are mainly stabilized by these interactions…

… [69]), that typically use physics-based and/or geometric … interaction energy and high surface
complementarity. The data-driven interface prediction methods include: (1) homology-based …

… The three-dimensional structure of an RNA molecule is to a large extent determined by
interactions between pairs of nucleotides, called base pairings. The secondary structure of an …

… the basic energetic terms that contribute to hot spot interactions, ie … predict hot spot residues
at protein-protein interfaces. Similarly to other energy-based methods, we consider the basic …