Abstract
Protein design software places amino acid side chains by precomputing rotamer-pair energies and optimizing rotamer placement. If the software optimizes by rapid stochastic techniques, then the precomputation phase dominates run time. We present a new algorithm for rapid rotamer-pair energy computation that uses a trie data structure. The trie structure avoids redundant energy computations, and lends itself to time-saving pruning techniques based on a simple geometric criteria. With our new algorithm, we compute rotamer-pair energies nearly 4 times faster than the previous approach.
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References
Looger, L.L., Dwyer, M.A., Smith, J.J., Hellinga, H.W.: Computational design of receptor and sensor proteins with novel functions. Nature 423, 185–190 (2003)
Dwyer, M., Looger, L., Hellinga, H.: Computational design of a biologically active enzyme. Science 304, 1967–1971 (2004)
Kuhlman, B., O’Niell, J.W., Kim, D.E., Zhang, K.Y., Baker, D.: Accurate computer-based design of a new backbone conformation in the second turn of protein L. J. Mol. Bio. 315, 471–477 (2002)
Kuhlman, B., Dantas, G., Ireton, G., Varani, G., Stoddard, B., Baker, D.: Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364–1368 (2003)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H.N.S.I., Bourne, P.: The protein data bank. Nucleic Acids Research 28, 235–242 (2000)
Butterfoss, G., Hermans, J.: Boltzmann-type distribution of side-chain conformation in proteins. Protein Science 12, 2719–2731 (2003)
Ponder, J.W., Richards, F.: Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Bio. 193, 775–791 (1987)
Dunbrack, R.L., Karplus Jr., M.: Backbone dependant rotamer library for proteins: application to side chain prediction. J. Mol. Bio. 230, 543–574 (1993)
Dunbrack Jr., R.L.: Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12, 431–440 (2002)
Lovell, S.C., Word, J.M., Richardson, J.S., Richardson, D.C.: The penultimate rotamer library. Proteins: Structure Function and Genetics 40, 389–408 (2000)
Desmet, J., Maeyer, M.D., Hazes, B., Lasters, I.: The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356, 539–541 (1992)
Goldstein, R.F.: Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophysical Journal 66, 1335–1340 (1994)
Looger, L.L., Hellinga, H.W.: Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J Mol Biol 307, 429–445 (2001)
Gordon, D., Mayo, S.: Branch-and-terminate: a combinatorial optimization algorithm for protein design. Structure Fold Des 7, 1089–1098 (1999)
Leaver-Fay, A., Kuhlman, B., Snoeyink, J.: An adaptive dynamic programming algorithm for the side chain placement problem. In: Pacific Symposium on Biocomputing, pp. 17–28. The Big Island, HI (2005)
Pierce, N., Winfree, E.: Protein design is NP-hard. Protein Engineering 15, 779–782 (2002)
Bradley, P., Chivian, D., Meiler, J., Misura, K., Rohl, C., Schief, W., Wedemeyer, W., Schueler-Furman, O., Murphy, P., Strauss, C., Schonbrun, J., Baker, D.: Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation. Proteins: Structure Function and Genetics 53, 457–468 (2003)
Dahiyat, B.I., Mayo, S.L.: De novo protein design: fully automated sequence selection. Science 278, 82–87 (1997)
Holm, L., Sander, C.: Fast and simple monte carlo algorithm for side chain optimization in proteins: application to model building by homology. Proteins 14, 213–223 (1992)
Saven, J.G., Wolynes, P.G.: Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules. J. Phys. Chem. B 101, 8375–8389 (1997)
Desjarlais, J.R., Handel, T.M.: De novo design of the hydrophobic cores of proteins. Protein Science 4, 2006–2018 (1995)
Weiner, P.: Linear pattern matching algorithms. In: Proc. 14th IEEE Annual Symp. on Switching and Automata Theory, pp. 1–11 (1973)
McCreight, E.M.: A space-economical suffix tree construction algorithm. Jrnl. of Algorithms 23, 262–272 (1976)
Ukkonen, E.: On-line construction of suffix trees. Algorithmica 14, 249–260 (1995)
Hellinga, H., Richards, F.: Construction of new ligand binding sites in proteins of known structure. I: Computer-aided modeling of sites with pre-defined geometry. J. Mol. Bio 222, 763–785 (1991)
Lazaridis, T., Karplus, M.: Effective energy function for proteins in solution. Proteins: Structure Function and Genetics 35, 133–152 (1999)
Kortemme, T., Morozov, A.V., Baker, D.: An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Bio. 326, 1239–1259 (2003)
Noonan, K., O’Brien, D., Snoeyink, J.: Probik: Protein backbone motion by inverse kinematics. In: WAFR 2004, Utrecht/Zeist, The Netherlands (2004)
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Leaver-Fay, A., Kuhlman, B., Snoeyink, J. (2005). Rotamer-Pair Energy Calculations Using a Trie Data Structure. In: Casadio, R., Myers, G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science(), vol 3692. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557067_32
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DOI: https://doi.org/10.1007/11557067_32
Publisher Name: Springer, Berlin, Heidelberg
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