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David Shortle. 2003. Propensities, probabilities, and the Boltzman hypothesis. Protein Science. [BIO] google scholar
Geng Wu Guozhou Xu Brenda A. and Nikola P. Pavletich. 2003. Structure of a Beta-TrCP1-Skp1-Beta-Catenin Complex: Destruction Motif Binding and Lysine Specificity of the SCF(beta-TrCP1) Ubiquitin Ligase. Molecular Cell. [BIO] google scholar
J. T. Huang and M. T. Wang. 2002. Secondary Structural Wobble: The Limits of Protein Prediction Accuracy. Biochemical and Biophysical Research Communications, vol 294, no 3, pp 621--625, June. [BIO] google scholar
A. Kloczkowski, K. L. Ting, RL Jernigan and J. Garnier. 2002. Combining the GOR V Algorithm with Evolutionary Information for Protein Secondary Structure Prediction from Amino Acid Sequence. PSFG, vol 49, pp 154--166. [BIO] google scholar
R. Matthew Fesinmeyer Jonathan W. Neidigh and Niels H. Andersen. 2002. Designing a 20-residue protein. Nature Structural Biology. [BIO] google scholar
Thomas A. Graham Wilson K. Cl and Wenqing Xu. 2002. The Crystal Structure of the Beta-Catenin/ICAT Complex Reveals the Inhibitory Mechanism of ICAT. Molecular Cell. [BIO] google scholar
Dimitrij Frishman. 2002. Knowledge-based selection of targets for structural genomics. Protein Engineering. [BIO] google scholar
Linlin Qiu Suzette A. Pabit and Stephen J. Hagen. 2002. Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 miliseconds. J. Am. Chem. Soc.. [BIO] google scholar
Minghua Deng , Shipra Mehta , Fengzhu Sun and Ting Chen . 2002. Inferring Domain-Domain Interactions from Protein-Protein Interactions. In RECOMB. [BIO] google scholar
K. Satou T. Oyama K. Kitano and T. Ito. 2002. Extraction of knowledge on protein-protein interaction by association rule discovery. Bioinformatics. [BIO] google scholar
E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai and A. L. Barabasi. 2002. Hierarchical Organization of Modularity in Metabolic Networks. Science. [BIO] google scholar
Carlos Simmerling Bentley Str and Adrian E. Roitberg. 2002. All-Atom Structure Prediction and Folding Simulations of a Stable Protein. J. Am. Chem. Soc.. [BIO] google scholar
Burkhard Rost. 2001. Review: Protein Secondary Structure Prediction Continues to Rise. JSB, vol 134, pp 204--218. [BIO] google scholar
David Kimelman Thomas A. Graham Denise M. Fe and Wenqing Xu. 2001. Tcf4 can specifically recognize beta-catenin using alternative conformations. In Nature Structural Biology. [BIO] google scholar
Joel R. Bock and David A. Gough. 2001. Predicting protein-protein interactions from primary structure. Bioinformatics. [BIO] google scholar
Steven L. Kazmirski Kam-Bo Wo and Valerie Daggett. 2001. Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution. PNAS. [BIO] google scholar
Shaw-Hwa Lo Shawn M. Gomez and Andrey Rzhetsky. 2001. Probabilistic Prediction of Unknown Metabolic and Signal-Transduction Networks. Genetics. [BIO] google scholar
Rohit V. Pappu Rajgopal Srini and George D. Rose. 2000. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding. PNAS. [BIO] google scholar
Thomas A. Graham Carole Weave and Wenqing Xu. 2000. Crystal Structure of a Beta-Catenin/Tcf Complex. In Cell. [BIO] google scholar
Trinh Xuan Hoang and Marek Cieplak. 2000. Sequencing of folding events in Go-type proteins. Journal of Chemical Physics. [BIO] google scholar
Cristian Micheletti Flavio Se and Amos Maritan. 2000. Recurrent Oligomers in Proteins: An Optional Scheme Reconciling Accurate and Concise Backbone Representations in Automated Folding and Design Studies. PROTEINS: Structure, Function, and Genetics. [BIO] google scholar
Irene Jacoboni Pier Luigi Mar and Rita Casadio. 2000. Predictions of Protein Segments With the Same Aminoacid Sequence and Different Secondary Structure: A Benchmark for Predictive Methods. PROTEINS: Structure, Function, and Genetics. [BIO] google scholar
Burkhard Rost and C. Sander. 2000. Third Generation Prediction of Secondary Structure. In Protein Structure Prediction: Methods and Protocols, pp 71--95, Clifton, NJ. Humana Press. [BIO] google scholar
Kim T. Simons Ingo Ruczinski and David Baker. 1999. Improved Recognition of Native-Like Protein Structures Using a Combination of Sequence-Dependent and Sequence-Independent Features of Proteins. PROTEINS: Structure, Function, and Genetics. [BIO] google scholar
Alexander D. MacKerell Jr.. 1999. CHARMM22 All-Hydrogen Topology File for Proteins. [BIO] google scholar
Oxana V. Galzitskaya and Alexei V. Finkelstein. 1999. A theoretical search for folding/unfolding nuclei in three dimensional protein structures. PNAS. [BIO] google scholar
P. Baldi, S. Brunak, P. Frasconi, G. Soda and G. Pollastri. 1999. Exploiting the Past and the Future in Protein Secondary Structure Prediction. Bioinformatics, vol 15, pp 937--946. [BIO] google scholar
James A. Cuff and Geoffrey J. Barton. 1999. Evaluation and Improvement of Multiple Sequence Methods for Protein Secondary Structure Prediction. PSFG, vol 34, pp 508--519. [BIO] google scholar
Robert L. Baldwin and George D. Rose. 1999. Is protein folding hierachic? 2. Folding intermediates and transition states. TIBS. [BIO] google scholar
Canan Baysal and Hagai Meirovitch. 1999. Efficiency of Simulated Annealing for Peptides With Increasing Geometrical Restrictions. Journal of Computational Chemistry. [BIO] google scholar
James A. Cuff, M. E. Clamp, A. S. Siddiqui, M. Finlay and Geoffrey J. Barton. 1998. Jpred: A Consensus Secondary Structure Prediction Server. Bioinformatics, vol 14, pp 892--893. [BIO] google scholar
I. Bahar M. Kaplan and RL Jernigan. 1997. Short-Range Conformational Energies, Secondary Structure Propensities, and Recognition of Correct Sequence-Structure Matches. PROTEINS: Sturcture, Function, and Genetics. [BIO] google scholar
A. A. Salamov and V. V. Solovyev. 1997. Protein Secondary Structure Prediction Using Local Alignments. JMB, vol 268, pp 31--36. [BIO] google scholar
Dimitrij Frishman and P. Argos. 1997. Seventy-five Percent Accuracy in Protein Secondary Structure Prediction. Proteins: Structure, Function, and Genetics, vol 27, pp 329--335. [BIO] google scholar
S. Altschul, et al. 1997. Gapped Blast and PSI-Blast: A New Generation of Protein Database Search Programs. NAR, vol 25, pp 3389--3402. [BIO] google scholar
Christopher Bystroff and David Baker. 1997. Blind Predictions of Local Protein Structure in CASP2 Targets Using the I-Sites Library. PROTEINS: Structure, Function, and Genetics. [BIO] google scholar
Paul D. Thomas and Ken A. Dill. 1996. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. USA. [BIO] google scholar
Paul D. Thomas and Ken A. Dill. 1996. Statistical Potentials Extracted From Protein Structures: How Accurate Are They?. JMB(J. Mol. Biol.). [BIO] google scholar
Karen F. Han and David Baker. 1996. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc. Natl. Acad. Sci. USA. [BIO] google scholar
R. D. King and M. J. E. Sternberg. 1996. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci, vol 5, pp 2298--2310. [BIO] google scholar
A. A. Salamov and V. V. Solovyev. 1995. Prediction of Protein Secondary Structure by Combining Nearest-Neighbor Algorithms and Multiple Sequence Alignments. JMB, vol 247, pp 11--15. [BIO] google scholar
Karen F. Han and David Baker. 1995. Recurring Local Sequence Motifs in Proteins. JMB(J. Mol. Biol.). [BIO] google scholar
Robert E. Bruccoleri. 1994. Conformational Search and Protein Folding. The Protein Folding Problem and Tertiary Structure Prediction. [BIO] google scholar
J. M. Levin, S. Pascarella, P. Argos and J. Garnier. 1993. Quantification of secondary structure prediction improvement using multiple alignment. Prot. Engin., vol 6, pp 849--854. [BIO] google scholar
Burkhard Rost and C. Sander. 1993. Prediction of Protein Secondary Structure at Better than 70% Accuracy. JMB, vol 232, pp 584--599. [BIO] google scholar
Sanzo Miyazawa and Robert L. Jernigan. 1983. Estimation of Effective Interresidue Contact Energies from Protein Crystal Structures: Quasi-Chemical Approximation. In Macromolecules. [BIO] google scholar
P.J. Flory. 1974. Foundations of Rotational Isomeric State Theory and General Methods for Generating Configurational Averages. Macromolecules. [BIO] google scholar
P. Y. Chou and G. D. Fasman. 1974. Conformational Parameters for Amino Acids in Helical, Beta Sheet and Random Coil Regions Calculated from Proteins. Biochemistry, vol 13, no 2, pp 211--222. [BIO] google scholar
Marek Cieplak Trinh Xuan Hoang Flavio Seno and Amos Maritan. Assembly of protein tertiary structures from secondary structures using optimized potentials. [BIO] google scholar

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