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Protein Surfaces and Solvent Accessibility: Definition and Prediction Jan Hansen, Ole Lund, Henrik Nielsen, Hans Henrik Stærfeldt, and Søren Brunak, Center for Biological Sequence Analysis, The Technical University of Denmark The surface of a protein is non-trivial to define, even when the structure is known. A widely used measure is the relative solvent accessibility, which denotes how large a part of the van der Waal's surface of each amino acid residue is exposed to the solvent surrounding the protein. Prediction of this quantity is important for predicting active sites, antibody epitopes, and post-translational modifications. The value of the relative solvent accessibility, however, is very dependent on parameters used for calculating it from the three-dimensional structure, mainly the sphere size. I will show accessibility distributions for various residues over a range of sphere sizes, and I will discuss problems such as multimeric proteins, internal cavities, and incomplete sequences. Prediction of solvent accessibility has been performed with artificial neural networks and statistical methods. I will describe a neural network approach currently under development in our group, and compare it to previously published methods. In particular, I will discuss the question of how much information can be extracted from the local sequence context, and the issue of single sequence versus profile prediction. ## Back to the list of abstracts