Ab initio prediction of protein structure using LINUS

LINUS is an ab initio method for the prediction of protein structure based on simple physical principles. Here we report the performance of LINUS at CASP4, a communitywide experiment to predict protein structure in which participants are blinded to the structures they seek to predict. We submitted 13 predictions for this experiment. The best four are described in detail, together with an assessment of secondary structure prediction for the entire set. Coordinates for all predictions are available from the CASP web site (http://predictionscenter.llnl.gov). It should be emphasized that our use of the descriptor "ab initio" is unequivocal: the sole input into these simulations is the amino acid sequence.