@article {Skolnick2003, title = {TOUCHSTONE: a unified approach to protein structure prediction.}, journal = {Proteins}, volume = {CASP Suppl}, number = {May}, year = {2003}, month = {jan}, pages = {469{\textendash}79}, abstract = {We have applied the TOUCHSTONE structure prediction algorithm that spans the range from homology modeling to ab initio folding to all protein targets in CASP5. Using our threading algorithm PROSPECTOR that does not utilize input from metaservers, one threads against a representative set of PDB templates. If a template is significantly hit, Generalized Comparative Modeling designed to span the range from closely to distantly related proteins from the template is done. This involves freezing the aligned regions and relaxing the remaining structure to accommodate insertions or deletions with respect to the template. For all targets, consensus predicted side chain contacts from at least weakly threading templates are pooled and incorporated into ab initio folding. Often, TOUCHSTONE performs well in the CM to FR categories, with PROSPECTOR showing significant ability to identify analogous templates. When ab initio folding is done, frequently the best models are closer to the native state than the initial template. Among the particularly good predictions are T0130 in the CM/FR category, T0138 in the FR(H) category, T0135 in the FR(A) category, T0170 in the FR/NF category and T0181 in the NF category. Improvements in the approach are needed in the FR/NF and NF categories. Nevertheless, TOUCHSTONE was one of the best performing algorithms over all categories in CASP5.}, keywords = {Algorithms, Models, Molecular, Protein Conformation, Protein Structure, Proteins, Proteins: chemistry, Secondary, Tertiary}, issn = {1097-0134}, doi = {10.1002/prot.10551}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14579335}, author = {Jeffrey Skolnick and Zhang, Yang and Arakaki, Adrian K and Andrzej Koli{\'n}ski and Michal Boniecki and Szil{\'a}gyi, Andr{\'a}s and Daisuke Kihara} } @article {Kihara2001, title = {TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {18}, year = {2001}, month = {aug}, pages = {10125{\textendash}30}, abstract = {The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab initio folding. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Furthermore, to generate representative protein structures, a reduced lattice-based protein model is used with replica exchange Monte Carlo to explore conformational space. We report results on the application of this methodology, termed TOUCHSTONE, to 65 proteins whose lengths range from 39 to 146 residues. For 47 (40) proteins, a cluster centroid whose rms deviation from native is below 6.5 (5) A is found in one of the five lowest energy centroids. The number of correctly predicted proteins increases to 50 when atomic detail is added and a knowledge-based atomic potential is combined with clustered and nonclustered structures for candidate selection. The combination of the ratio of the relative number of contacts to the protein length and the number of clusters generated by the folding algorithm is a reliable indicator of the likelihood of successful fold prediction, thereby opening the way for genome-scale ab initio folding.}, keywords = {Algorithms, Computer Simulation, Models, Molecular, Monte Carlo Method, Protein Folding, Protein Structure, Proteins, Proteins: chemistry, Tertiary}, issn = {0027-8424}, doi = {10.1073/pnas.181328398}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=56926\&tool=pmcentrez\&rendertype=abstract}, author = {Daisuke Kihara and Hui Lu and Andrzej Koli{\'n}ski and Jeffrey Skolnick} }