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sb120317.qxd 24/05/02 16:00 Page 348 348 Protein structure prediction in 2002 Jack Schonbrun, William J Wedemeyer and David Baker* Central issues concerning protein structure prediction have Traditionally, protein structure prediction is divided into been highlighted by the recently published summary of the three areas, depending on the similarity of the target to fourth community-wide protein structure prediction experiment proteins of known structure. First, in comparative modeling, (CASP4). Although sequence/structure alignment remains one or more template proteins of known structure with the bottleneck in comparative modeling, there has been high sequence homology to the target sequence are substantial progress in fully automated remote homolog identified. The target and template sequences are aligned, detection and in de novo structure prediction. Significant and a three-dimensional structure of the target protein is further progress will probably require improvements in generated from the coordinates of the aligned residues of high-resolution modeling. the template protein, combined with models for loop regions and other unaligned segments. Ideally, this three- Addresses dimensional model would then be refined to bring it closer Howard Hughes Medical Institute and Department of Biochemistry, to the true structure of the target protein. A key outstanding