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Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete.
Berger B, Leighton T. Berger B, et al. J Comput Biol. 1998 Spring;5(1):27-40. doi: 10.1089/cmb.1998.5.27. J Comput Biol. 1998. PMID: 9541869
Algorithms for protein structural motif recognition.
Berger B. Berger B. J Comput Biol. 1995 Spring;2(1):125-38. doi: 10.1089/cmb.1995.2.125. J Comput Biol. 1995. PMID: 7497115
Predicting coiled coils by use of pairwise residue correlations.
Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS. Berger B, et al. Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8259-63. doi: 10.1073/pnas.92.18.8259. Proc Natl Acad Sci U S A. 1995. PMID: 7667278 Free PMC article.
MultiCoil: a program for predicting two- and three-stranded coiled coils.
Wolf E, Kim PS, Berger B. Wolf E, et al. Protein Sci. 1997 Jun;6(6):1179-89. doi: 10.1002/pro.5560060606. Protein Sci. 1997. PMID: 9194178 Free PMC article.
An iterative method for improved protein structural motif recognition.
Berger B, Singh M. Berger B, et al. J Comput Biol. 1997 Fall;4(3):261-73. doi: 10.1089/cmb.1997.4.261. J Comput Biol. 1997. PMID: 9278059
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains.
Singh M, Berger B, Kim PS, Berger JM, Cochran AG. Singh M, et al. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2738-43. doi: 10.1073/pnas.95.6.2738. Proc Natl Acad Sci U S A. 1998. PMID: 9501159 Free PMC article.
Local rules simulation of the kinetics of virus capsid self-assembly.
Schwartz R, Shor PW, Prevelige PE Jr, Berger B. Schwartz R, et al. Biophys J. 1998 Dec;75(6):2626-36. doi: 10.1016/S0006-3495(98)77708-2. Biophys J. 1998. PMID: 9826587 Free PMC article.
On the structure of the scaffolding core of bacteriophage T4.
Berger B, Hoest GW, Paulson JR, Shor PW. Berger B, et al. J Comput Biol. 1999 Spring;6(1):1-12. doi: 10.1089/cmb.1999.6.1. J Comput Biol. 1999. PMID: 10223661
A dictionary-based approach for gene annotation.
Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. Pachter L, et al. J Comput Biol. 1999 Fall-Winter;6(3-4):419-30. doi: 10.1089/106652799318364. J Comput Biol. 1999. PMID: 10582576
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