A new method for exact analytical calculation of the accessible surface areas and their
gradients with respect to atomic coordinates is described. The new surface routine�…

An algorithm for the rapid analytical determination of the accessible surface areas of solute
molecules is described. The accessible surface areas as well as the derivatives with respect�…

A fast analytical formula (TDND) has been derived for the calculation of approximate atomic
and molecular solvent-accessible surface areas (SASA), as well as the first and second�…

We present a CPU efficient protocol for refinement of protein structures in a thin layer of
explicit solvent and energy parameters with completely revised dihedral angle terms. Our�…

We analyze the contact distance distributions between nonbonded atoms in known protein
structures. A complete set of van der Waals (VDW) radii for 24 protein atom types and for�…

Contact surface area and chemical properties of atoms are used to concurrently predict
conformations of multiple amino acid side chains on a fixed protein backbone. The�…

Abstract POPS (Parameter OPtimsed Surfaces) is a new method to calculate solvent
accessible surface areas, which is based on an empirically parameterisable analytical�…

An efficient method for calculating the free energy of solvation of a (macro) molecule
embedded in a continuum solvent is presented. It is based on the fully analytical evaluation�…

The burial of hydrophobic amino acids in the protein core is a driving force in protein folding.
The extent to which an amino acid interacts with the solvent and the protein core is naturally�…

The quantification of the packing of residues in proteins and docking of ligands to
macromolecules is important in understanding protein stability and drug design. The number�…