All_Papers

Michael Levitt's Publications in Chronological Order (May 2004)

A paper Levitt considers to be one of his twenty best is marked [a]; a paper he considers to be of his ten best is marked [a+].

Levitt, M. and S. Lifson. Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure. J. Mol. Biol. 46, 269-279 (1969). [a] [PDF File 1206K]
Levitt, M. Detailed Molecular Model for Transfer Ribonucleic Acid. Nature 224, 759-763 (1969). [a] [PDF File 392K]
Warshel, A., M. Levitt and S. Lifson. Consistent Force Field for Calculation of Vibrational Spectra and Conformations of Some Amides and Lactam Rings. J. Mol. Spect. 33, 84-98 (1970)
Levitt, M. Folding of Nucleic Acids. In Polymerization in Biological Systems, Ciba Foundation Symposium 7, Elsevier, Amsterdam, pp. 146-171 (1972). [PDF File 502K]
Levitt, M. Orientation of Double-Helical Segments in Crystals of Yeast Phenylalanine Transfer RNA. J. Mol. Biol. 80, 255-263 (1973).
Levitt, M. Energy Refinement of Hen Egg-White Lysozyme. J. Mol. Biol. 82, 393-420 (1974).
Levitt, M. On the Nature of the Binding of Hexa-N-Acetyl Glucosamine Substrate to Lysozyme. In Peptides, Polypeptides and Proteins, Wiley, New York, pp. 99-113 (1974).
Schulz, G. E., C. D. Barry, J. Friedman, P. Y. Chou, G. D. Fasman, A. V. Finkelstein, V. I. Lim, O. B. Ptitsyn, E. A. Kabat, T. T. Wu, M. Levitt, B. Robson and K. Nagano. Comparison of Predicted and Experimentally Determined Secondary Structure of Adenylate Kinase. Nature 250, 140-142 (1974) [PDF file 156K]
Levitt, M. and A. Warshel. Computer Simulation of Protein Folding. Nature 253, 694-698 (1975). [a+] [PDF file 176K]
Warshel, A. and M. Levitt. Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme. J. Mol. Biol. 103, 227-249 (1976). [a+] [PDF file 1211K]
Levitt, M. A Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. J. Mol. Biol. 104, 59-107 (1976). [a+] [PDF file 2784K]
Levitt, M. and C. Chothia. Structural Patterns in Globular Proteins. Nature 261, 552-558 (1976). [a+] [PDF file 452K]
Warshel, A. and M. Levitt. Folding and Stability of Helical Proteins: Carp Myogen. J. Mol. Biol. 106, 421-437 (1976).
Levitt, M. SECAM Workshop “Models for Protein Dynamics” The Dynamics Behavior of a Simplified Representation of Pancreatic Trypsin Inhibitor. pp. 220-228. (1976) [PDF file 1430K]
Levitt, M. and J. Greer. Automatic Identification of Secondary Structure in Globular Proteins. J. Mol. Biol. 114, 181-239 (1977). [PDF file 4657K]
Chothia, C., M. Levitt and D. Richardson. Structure of Proteins: Packing of a-Helices and Pleated Sheets. Proc. Nat. Acad. Sci. USA 74, 4130-4134 (1977). [PDF file 369K]
Finch, J. T., L. C. Lutter, D. Rhodes, R. S. Brown, B. Rushton, M. Levitt and A. Klug. Structure of the Nucleosome Core Particles of Chromatin. Nature 269, 29-35 (1977).
Levitt, M. Protein Folding as a Random Walk. Proceedings of the 7-th Taniguichi Symposium, 1977. [PDF file 721K]
Levitt, M. and A. Warshel. Extreme Conformational Flexibility of the Furanose Ring in DNA and RNA. J. Am. Chem. Soc. 100, 2607-2613 (1978). [PDF file 541K]
Jack, A. and M. Levitt. Refinement of Large Structures by Simultaneous Minimization of Energy and R Factor. Acta Crystallogr. A34, 931-935 (1978). [a] [PDF file 239K]
Levitt, M. How Many Base-Pairs per Turn Does DNA have in Solution and in Chromatin? Some Theoretical Calculations. Proc. Nat. Acad. Sci. USA 75, 640-644 (1978). [a] [PDF file 354K]
Levitt, M. Conformational Preferences of Amino Acids in Globular Proteins. Biochemistry 17, 4277-4285 (1978). [PDF file 462K]
Janin, J., S. Wodak, M. Levitt and B. Maigret. The Conformation of Amino Acid Side Chains in Proteins. J. Mol. Biol. 125, 357-386 (1978).
Prunell, A., R. D. Kornberg, L. Lutter, A. Klug, M. Levitt and F. H. C. Crick. Periodicity of Deoxyribonuclease I Digestion of Chromatin. Science 204, 855-858 (1979). [PDF file 980K]
Lifson, S. and M. Levitt. On Obtaining Energy Parameters from Crystal Structure Data. Computers and Chemistry 3, 49-51 (1979).
Levitt, M. Computer Studies of Protein Molecules. In Protein Folding, Elsevier/North Holland, pp. 17-40 (1980).
Levitt, M. Effect of Proline Residues on Protein Folding. J. Mol. Biol. 145, 251-263 (1981). [PDF file 995K]
Chothia, C., M. Levitt and D. Richardson. Helix to Helix Packing in Proteins. J. Mol. Biol. 145, 215-250 (1981).
Levitt, M. The Molecular Dynamics of Hydrogen Bonds in Bovine Pancreatic Trypsin Inhibitor Protein. Nature 294, 379-380 (1981).
Levitt, M. Hydrogen Bond and Internal Solvent Dynamics of BPTI Protein. Ann. NY Acad. Sci.. 367, 162-181 (1981).
Levitt, M., and R.J. Feldmann. Conformational Dynamics of Pancreatic Trypsin Inhibitor: A Movie. In Structural Aspects of Recognition and Assembly in Biological Macromolecules, Elsevier/North Holland (1981).
Levitt, M. Protein Conformation, Dynamics and Folding by Computer Simulation. Ann. Rev. Biophys. Bioeng. 11, 251-271 (1982).
Levitt, M. Computer Simulation of DNA Double Helix Dynamics. Cold Spring Harbor Symp. Quant. Biol. 47, 251-261 (1983). [PDF file 730K]
Levitt, M. Molecular Dynamics of Native Protein: I. Computer Simulation of Trajectories. J. Mol. Biol. 168, 595-620 (1983). [a] [PDF file 1733K]
Levitt, M. Molecular Dynamics of Native Protein: II. Analysis and Nature of Motion. J. Mol. Biol. 168, 595-620 (1983). [a] [PDF file 1733K]
Levitt, M. Protein Folding by Restrained Energy Minimization and Molecular Dynamics. J. Mol. Biol. 170, 723-764 (1983). [a+] [PDF file 1671K]
Levitt, M., Sander, C. and Stern, P.S. Normal-Mode Dynamics of a Protein: Bovine Pancreatic Trypsin Inhibitor. Int. J. Quant. Chem: Quant. Biol. Symp., 10, 181-199 (1983).
Henry, E. R., M. Levitt and W. A. Eaton. Molecular Dynamics Simulation of Photodissociation of Carbon Monoxide from Hemoglobin. Proc. Natl. Acad. Sci. USA, 82, 2034-2038 (1985). [PDF file 305K]
Levitt, M., C. Sander and P. S Stern. Protein Normal-Mode Dynamics: Trypsin Inhibitor, Crambin, Ribonuclease and Lysozyme. J. Mol. Biol. 181, 423-447 (1985). [a] [PDF file 413K]
Pattabiraman, N., M. Levitt, T. E. Ferrin and Langridge, R. Computer Graphics in Real Time Docking with Energy Calculations and Minimization, J. Comput. Chem. 6, 432-436 (1985). [PDF file 1089K]
Chothia, C., A. M. Lesk, M. Levitt, A. G. Amit, R. A. Mariuzza, S. E. V. Phillips and R. J. Poljak. The Predicted Structure of Immunoglobulin D1.3 and Its Comparison with the Crystal Structure. Science, 233, 755-758 (1986)
Lesk, A. M., M. Levitt and C. Chothia. Alignment of the Amino Acid Sequences of Distantly Related Proteins Using Variable Gap Penalties. Protein Engineering, 1, 77-78 (1986). [PDF file 311K]
Levitt, M., and R. Sharon. Simulating Protein Dynamics in Solution. In Crystallography in Molecular Biology, ed. Moras D. et al. NATO ASI Series A: Life Sciences, Vol. 126, pp. 197-207 (1987).
Anglister, J., M. Bond, T. Frey, D. Leahy, M. Levitt, H. M. McConnell and M. Whittaker. Contribution of Tryptophan Residues to the Combining Site of a Monoclonal Anti-Dinitrophenyl Spin-Label Antibody. Biochemistry, 26, 6058-6064 (1987).
Levitt, M. and M. F. Perutz. Aromatic Rings Act as Hydrogen Bond Acceptors. J. Mol. Biol. 201, 751-754 (1988). [a] [PDF file 186K]
Levitt, M. and R. Sharon. Accurate Simulation of Protein Dynamics in Solution. Proc. Natl. Acad. Sci. USA. 85, 7557-7561 (1988). [a+] [PDF file 413K]
Levitt, M. A Calculated Conformation for the Folding Transition State of Bovine Pancreatic Trypsin Inhibitor. In Protein Structure and Protein Engineering, ed. Winnacker E. L. and Huber, R. Springer-Verlag, Berlin, Heidelberg pp. 45-50 (1988).
Levitt, M. Molecular Dynamics of Macromolecules in Water. Chemica Scripta, 29A, 197-203 (1989).
Levy, R., O. Assulin, T. Scherf, M. Levitt and J. Anglister. Probing Antibody Diversity by 2D NMR: Comparison of Amino Acid Sequences, Predicted Structures and Observed Antibody-Antigen Interactions in Complexes of Two Antipeptide Antibodies. Biochemistry, 28, 7168-7175 (1989).
Matsumura, M., W. J. Becktel, M. Levitt and B. W. Matthews. Stabilization of Phage T4 Lysozyme by Engineered Disulfide Bonds. Proc. Natl. Acad. Sci. USA. 86, 6562-6566 (1989). [PDF file 413K]
Chothia, C., A. M. Lesk, M. Levitt, A. Tramontano, S. J. Smith-Gill, G. Air, S. Sheriff, E. A. Padlan, D. Davies, W. R. Tulip and P. M. Colman. The Conformations of Immunoglobulin Hypervariable Regions. Nature, 342, 877-883 (1989).
Queen, C., W. P. Schneider, H. E. Selick, P. W. Payne, N. F. Landolfi, J. F. Duncan, N. M. Avdalovic, M. Levitt, R. P. Junghans and T. A. Waldmann. A Humanized Antibody that Binds to the IL-2 Receptor. Proc. Natl. Acad. Sci. USA. 86, 10029-10033 (1989).
Zilber, B., T. Scherf, M. Levitt and J. Anglister. NMR Derived Model for a Peptide-Antibody Complex. Biochemistry, 29, 10032-10041 (1990).
Levitt, M. Protein Folding. Curr. Opinions Struct. Biol. 1, 224-229 (1991).
Lee, C. and M. Levitt. Accurate Prediction of the Stability and Activity Effects of Site-directed Mutagenesis of a Protein Core. Nature, 352, 448-451 (1991). [PDF file 204K]
Levitt, M. Real-Time Interactive Frequency Filtering of Molecular Dynamics Trajectories. J. Mol. Biol. 220, 1-4 (1991).
Theriault, T. P, G. S. Rule, D. J. Leahy, M. Levitt and H. M. McConnell. Structural and Kinetic Studies of the Fab Fragment of a Monoclonal Anti-Spin Label Antibody by NMR. J. Mol. Biol. 221, 257-270 (1991).
Daggett, V. and M. Levitt. A Molecular Dynamics Simulation of the C-Terminal Fragment of the L7/L12 Ribosomal Protein in Solution. Chemical Phys. 158, 501-512 (1991).
Narhi, L. O., Y. Stabinsky, M. Levitt, L. Miller, R. Sachdev, S. Finley, S. Park, C. Kolvenbach, T. Arakawa and M. Zukowski. Enhanced stability of subtilisin by three point mutations. Biotechnology and Applied Biochemistry 1, 12-24 (1991).
Daggett, V. and M. Levitt. Molecular Dynamics Simulation of Helix Denaturation. J. Mol. Biol. 223, 1121-1138 (1992). [PDF file 1163K] [PDF file 1163K]
Hinds, D. A. and M. Levitt. A Lattice Model for Protein Structure Prediction at Low Resolution. Proc. Natl. Acad. Sci. USA. 89, 2536-2540 (1992). [PDF file 501K]
Levitt, M. Accurate Modelling of Protein Conformation by Automatic Segment Matching. J. Mol. Biol. 226, 507-533 (1992). [a+] [PDF file 2652K]
Daggett, V. and M. Levitt. Molecular Dynamics Simulation of the Molten Globule State. Proc. Natl. Acad. Sci. USA. 89, 5142-5146 (1992). [a+] [PDF file 740K]
Scherf, T., R. Hiller, F. Naider, M. Levitt and Y. Anglister. Induced Peptide Conformations in Different Antibody Complexes: Molecular Modelling of the Three-Dimensional Structure of Peptide-Antibody Complexes Using NMR Distance Restraints. Biochemistry 31, 6884-6897 (1992).
Subbiah, S., D. V. Laurents and M. Levitt. Structural Similarity of DNA-binding Domains of Bacteriophage Repressors and the Globin Core. Current Biol. 3, 141-148 (1993). [PDF file 718K]
Daggett, V. and M. Levitt. Realistic Simulation of Native Protein Dynamics in Solution and Beyond. Ann. Rev. Biophys & Biomol. Struct. 22, 353-380 (1993).
Daggett, V. and M. Levitt. Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations. J. Mol. Biol. 232, 600-618 (1993). [PDF file 1515K]
Levitt, M. and B. Park. Water: Now You See It, Now You Don't. Structure. 1 223-226 (1993). [PDF file 434K]
Daggett, V. and M. Levitt. Protein Folding <-> Unfolding Dynamics. Current Opinions in Structural Biology 4, 291-295 (1994).
Laurents, D. V., S. Subbiah and M. Levitt. Different Protein Sequences Can Give Rise to Highly Similar Folds Through Different Stabilizing Interactions. Protein Science 3, 1938-1944 (1994).
Hinds, D. A. and M. Levitt. Exploring Conformational Space with a Simple Lattice Model for Protein Structure. J. Mol. Biol. 243, 668-682 (1994). [a] [PDF file 1300K]
Hinds, D. A. and M. Levitt. Simulation of Protein-Folding Pathways: Lost in (Conformational) Space? Trends in Biotechnology. 13, 23-27 (1995).
Levitt, M., M. Hirshberg, R. Sharon and V. Daggett. Potential Energy Function and Parameters for Simulations of the Molecular Dynamics of Proteins and Nucleic Acids in Solution. Computer Physics Communications, 91, 215-231 (1995). [PDF file 616K]
Park, B. and M. Levitt. The Complexity and Accuracy of Discrete State Models of Protein Structure. J. Mol. Biol., 249, 493-507 (1995). [PDF file 657K]
Gerstein, M., J. Tsai and M. Levitt. The Volume of Atoms on the Protein Surface: Calculated from Simulation using Voronoi Polyhedra. J. Mol. Biol., 249, 955-966 (1995). [PDF file 497K]
Huang, E.S., S. Subbiah and M. Levitt. Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues. J. Mol. Biol., 252, 709-720 (1995). [PDF file 408K]
Shoham, S., T. Scherf, J. Anglister, M. Levitt, E. A. Merritt and W. G. J. Hol. Structural Diversity in a Conserved Cholera Toxin Epitope Involved in Ganglioside Binding. Protein Science, 4, 841-848 (1995).
Tsai, J., M. Gerstein and M. Levitt. Keeping the Shape but Changing the Charge: A Simulation Study of Urea and Its Iso-Steric Analogues. J. Chem. Phys., 104, 9417-9430 (1996). [PDF file 408K]
Huang, E.S., J. Tsai, S. Subbiah and M. Levitt. Using a Hydrophobic Contact Potential to Evaluate Native and Near-Native Folds Generated by Molecular Dynamics Simulations. J. Mol. Biol., 257, 716-725(1996). [PDF file 302K]
Hinds, D.A. and M. Levitt. From Structure to Sequence and Back Again. J. Mol. Biol., 258, 201-209 (1996). [PDF file 421K]
Park, B. and M. Levitt. Energy Functions that Discriminate X-ray and Near-Native Folds from Well-Constructed Decoys. J. Mol. Biol., 258, 367-392 (1996). [a+] [PDF file 2005K]
Zhou, Z., Payne, P., Vasquez, M., Kuhn, N. and M. Levitt. Finite-Difference Solution of the Poisson-Boltzmann Equation: Complete Elimination of Self-Energy. J. Comp. Chem.., 11, 1344-1351 (1996).
Park, B., Huang, E. S. and M. Levitt. Factors Affecting The Ability of Energy Functions to Discriminate Correct from Incorrect Folds. J. Mol. Biol., 266, 831-846 (1997). [PDF file 314K]
Levitt, M., Hirshberg, M., Sharon, R., Laidig, K.E., and Daggett, V. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution. J. Phys. Chem., B25, 5051-5061 (1997). [PDF file 380K]
Hirshberg, M. and M. Levitt. Simulating the Dynamics of the DNA Double Helix in Solution. In Dynamics and the Problem of Recognition in Biological Macromolecules, ed. Jardetzky, O. and Lefevre, J. Plenum Press, New York, pp. 173-191 (1997). [PDF file 904K]
Levitt, M., M. Gerstein, E.S. Huang, S. Subbiah and J. Tsai. Protein Folding: The End-Game. Ann. Rev. Biochemistry, 66, 549-579 (1997). [PDF file 168K]
Gerstein, M. and M. Levitt. A Structural Census of the Current World of Protein Sequences. Proc. Natl. Acad. Sci., 99, 11911-11916 (1997). [PDF file 244K]
Tsai, J., M. Gerstein, and M. Levitt. Simulating the Minimum Core for Hydrophobic Collapse in Globular Proteins. Protein Science, 6, 1-11 (1997). [PDF file 1673K]
Gerstein, M. and M. Levitt. Comprehensive Assessment of Automatic Structural Alignment against a Manual Standard, the SCOP Classification of Proteins. Protein Science, 7, 445-456 (1998). [PDF file 369K]
Levitt, M. Competitive Assessment of Protein Fold Recognition and Alignment Accuracy. Proteins, Struct., Funct. and Gen. Suppl, 1, 92-104 (1997). [PDF file 141K]
Marchler-Bauer, A., Levitt, M and S. Bryant. A Retrospective Analysis of the CASP2 Threading Predictions. Proteins, Struct., Funct. and Gen. Suppl, 1, 83-91 (1997). [PDF file 95K]
Levitt, M and M. Gerstein. A Unified Statistical Framework for Sequence Comparison and Structure Comparison. Proc. Natl. Acad. Sci., 95, 5913-5920 (1998). [PDF file 371K]
Gerstein, M. and M. Levitt. Simulating Water and the Molecules of Life. Scientific American, Nov 101-105 (1998). [PDF file 555K]
Lee, C. and M. Levitt. Packing as a Structural Basis of Protein Stability: Understanding Mutant Properties from Wildtype Structure. Pac. Symp. Biocomput. 245-255 (1998).
Huang, E.S., P. Koehl, M. Levitt, R.V. Pappu and J.W. Ponder. Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods. Proteins, 33:204-217 (1998). [PDF file 223K]
Samudrala, R., Xia, Y., Levitt, M. and E.S. Huang. A Combined Approach For Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence. Pac Symp Biocomput. 505-516 (1999). [PDF file 803K]
Brenner, S.E., D. Barken, and M. Levitt M. The PRESAGE Database for Structural Genomics. Nucleic Acids Res. 27:251-3 (1999). [PDF file 27K]
Koehl, P. and M. Levitt. A Brighter Future for Protein Structure Prediction. Nat Struct Biol. 6:108-111 (1999). [PDF file 209K]
Samudrala, R., Y. Xia, E.S. Huang, and M. Levitt. Bona Fide Ab Initio Protein Structure Prediction Using a Combined Hierarchical Approach. Proteins, Struct., Funct. and Gen. Suppl. 3S: 194-198 (1999). [PDF file 176K]
Tsai, J., M. Levitt and D. Baker. Hierarchy of Structure Loss in MD Simulations of SRC SH3 Domain Unfolding. J. Mol. Biol. 291: 215-225 (1999). [PDF file 628K]
Koehl, P. and M. Levitt. De Novo Protein Design. I. In Search of Stability and Specificity. J. Mol. Biol. 293: 1161-1181 (1999). [PDF file 372K]
Koehl, P. and M. Levitt. De Novo Protein Design. II. Plasticity in Sequence Space. J. Mol. Biol. 293: 1183-1193 (1999). [PDF file 210K]
Koehl P. and M. Levitt. Structure-Based Conformational Preferences of Amino Acids. Proc. Natl. Acad. Sci. U S A, 96:12524-12529 (1999). [PDF file 192K]
Brenner, S.E, Koehl, P. and M. Levitt. The Astral Compendium for Protein Structure and Sequence Analysis Nucleic Acids Res.,28:254-256 (2000). [PDF file 108K]
Brenner, S. E. and M. Levitt. Expectations from Structural Genomics. Protein Science, 9, 197-200 (2000). [PDF file 110K]
Samudrala, R, Xia Y, Levitt M, Cotton NJ, Huang ES, and R. Davis. Probing Structure-Function Relationships of the DNA Polymerase Alpha-Associated Zinc-Finger Protein Using Computational Approaches. Pac. Symp. Biocomput., 12, 179-190 (2000). [PDF file 3101K]
Yona, G. and M. Levitt. A Unified Sequence-Structure Classification of Protein Sequences: Combining Sequence and Structure in a Map of the Protein Space. RECOMB 2000, pp. 308-317, ACM (2000). [PDF file 940K]
Samudrala, R. Huang, E.S., Koehl, P. and M. Levitt. Constructing side chains on near-native main chains for ab initio protein structure prediction. Protein Eng. 3, 453-457 (2000). [PDF file 230K]
Xia, Y., Huang, E.S., Levitt, M. and Samudrala, R. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol., 300, 171-185 (2000). [PDF file 552K]
Samudrala R, Levitt M. Decoys 'R' Us: A database of incorrect protein conformations for evaluating scoring functions. Protein Science, 9: 1399-1401 (2000). [PDF file 92K]
Yona, G. and M. Levitt. Towards A Complete Map of the Protein Space Based on a Unified Sequence And Structure Analysis of All Known Proteins. Proceedings of ISMB. In Press (2000). [PDF file 396K]
Xia. Y. and M. Levitt. Extracting Knowledge-Based Energy Functions from Protein Structures by Error Rate Minimization: Comparison of Methods Using Lattice Model. J. Chem. Phys. 113, 9318-9330 (2000). [PDF file 284K]
Fain, B. and M. Levitt. A Novel Method for Sampling Alpha-helical Protein Backbones, J. Mol. Biol., 305, 191-201 (2001). [PDF file 582K]
Levitt, M. The Birth of Computational Structural Biology, Nature Str. Biol., 8, 392-393 (2001).[PDF file 330K]
Raschke, T.M., Tsai, J. and M. Levitt. Quantification of the Hydrophobic Interaction by Simulations of the Aggregation of Small Hydrophobic Solutes in Water. Proc. Natl. Acad. Sci., 98, 5965-5660 (2001). [a] [PDF file 304K]
Fain, B., Y. Xia, and M. Levitt. Determination of Optimal Chebyshev-Expanded Hydrophobic Discrimination Function for Globular Proteins. IBM J. Res. Dev. 45. 525-532 (2001). [PDF file 103K]
Chandonia, J.M., Walker N.S., Lo Conte L., Koehl P., Levitt M., and Brenner S.E. ASTRAL compendium enhancements. Nucleic Acids Res. 30: 260-263 (2002). [PDF file 83K]
Koehl, P. and M. Levitt. Improved Recognition of Native-Like Protein Structures Using a Family of Designed Sequences. Proc Natl. Acad. Sci U S A. 99: 691-696 (2002). [PDF file 272K]
Koehl, P. and M. Levitt. Protein Topology and Stability Define the Space of Allowed Sequences. Proc Natl. Acad. Sci U S A. 99: 1280-1285 (2002). [PDF file 378K]
Yona, G. and M. Levitt. Within the Twilight Zone: A Sensitive Profile-Profile Comparison Tool Based on Information Theory. J Mol Biol. 315: 1257-1275 (2002). [PDF file 757K]
Xia, Y and M. Levitt. Roles of Mutation and Recombination in the Evolution of Protein Thermodynamics. Proc Natl. Acad. Sci U S A. 99: 10382-10387 (2002). [a+] [PDF file 270K]
Fain, B., Xia, Y. and M. Levitt. Design of an Optimal Chebyshev-Expanded Discrimination Function for Globular Proteins. Protein Sci. 11: 2010-2021 (2002). [PDF file 214K]
Samudrala R. and M. Levitt. A Comprehensive Analysis of 40 Blind Protein Structure Predictions. BMC Struct. Biol. 2: 3-10 (2002). [PDF file 748K]
Kolodny, R., Koehl, P., Guibas, L., and M. Levitt. Small Libraries of Protein Fragments Model Native Protein Structures Accurately. J Mol Biol. 323:297-307 (2002). [PDF file 752K]
Koehl, P. and M. Levitt. Sequence Variations within Protein Families are Linearly Related to Structural Variations. J. Mol. Biol. 323:551-562 (2002). [PDF file 633K]
Kolodny, R. and M. Levitt. Protein Decoy Assembly Using Short Fragments under Geometric Constraints. Biopolymers, 68: 278-285 (2003). [PDF file 156K]
Tsai. J. and M. Levitt. Evidence of Turn and Salt Bridge Contributions to β-Hairpin Stability: MD Simulations of C-terminal Fragment from the B1 Domain of Protein G. Biophys. Chem.102:187-201 (2002). [PDF file 724K]
Keasar, C. and M. Levitt. A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics. J. Mol. Biol. 329, 159-174 (2003). [a] [PDF file 3632K]
Fain B, and M. Levitt M. Funnel Sculpting for in Silico Assembly of Secondary Structure Elements of Proteins. Proc Natl. Acad. Sci U S A. 100: 10700-10705 (2003). [PDF file 476K] [PDF Appendix 37K]
Chandonia J. M., Hon G., Walker N.S., Lo Conte L., Koehl P., Levitt M. and S.E. Brenner. The ASTRAL Compendium in 2004. Nucleic Acids Res. 32: 189-192 (2004). [PDF file 126K]
Xia,Y. and M. Levitt. Funnel-Like Organization in Sequence Space Determines the Distributions of Protein Stability and Folding Rate Preferred by Evolution. Proteins, 55: 107-114. [PDF file 724K]

Xia,Y. and M. Levitt. Simulating Protein Evolution in Sequence and Structure Space. Curr. Opin. Struct. Biol. 14: 202-207 (2004). [PDF file 133K]