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Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments. Journal of molecular biology. 277(2):419-48. PDF. 1998.
Computer simulations of de novo designed helical proteins. Biophysical journal. 75(1):92-105. PDF. 1998.
How do potentials derived from structural databases relate to "true" potentials? Protein science : a publication of the Protein Society. 7(1):112-22. PDF. 1998.
Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations. Proceedings of the National Academy of Sciences of the United States of America. 95(3):1020-5. PDF. 1998.
Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nature biotechnology. 16(8):753-6. PDF. 1998.
Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Folding & design. 3(6):535-48. PDF. 1998.
Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins. The Journal of Chemical Physics. 108(6):2608. PDF. 1998.
What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? Folding & design. 3(2):141-7. PDF. 1998.
A Synthetic Retrotransition (Backward Reading) Sequence of the Right-Handed Three-Helix Bundle Domain (10-53) of Protein A Shows Similarity in Confomation as Predicted by Computation. Journal of the American Chemical Society. 120(50):13042-13045. PDF. 1998.
An Efficient Monte Carlo Model of Protein Chains. Modeling the Short-Range Correlations between Side Group Centers of Mass. The Journal of Physical Chemistry B. 102(23):4628-4637. PDF. 1998.
What should the Z-score of native protein structures be? Protein Science. 7(5):1201-1207. PDF. 1998.
Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach. Journal of Computational Biology. 5(3):531-538. PDF. 1998.
Application of a high coordination lattice model in protein structure prediction. Workshop on Monte Carlo Approach to Biopolymers and Protein Folding. :377-388. PDF. 1998.
Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins. Pacific Symposium on Biocomputing (PSB-98). :377-388. PDF. 1998.
Monte Carlo approaches to the protein folding problem. Monte Carlo Methods in Chemical Physics. 105:203-242. PDF. 1998.
Protein Modeling. Encyclopedia of Computational Chemistry. :2200-2211.. 1998.
A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. Annual International Conference on Research in Computational Molecular Biology (RECOMB98) . :214-220. PDF. 1998.
Recognition of protein structure on coarse lattices with residue-residue energy functions. Protein engineering. 10(10):1123-30. PDF. 1997.
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein science : a publication of the Protein Society. 6(3):676-88. PDF. 1997.
MONSSTER: a method for folding globular proteins with a small number of distance restraints. Journal of molecular biology. 265(2):217-41. PDF. 1997.
A method for the prediction of surface "U"-turns and transglobular connections in small proteins. Proteins. 27(2):290-308. PDF. 1997.
Sequence-structure specificity--how does an inverse folding approach work? Protein engineering. 10(4):317-31. PDF. 1997.
Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions. The Journal of Chemical Physics. 107(3):953. PDF. 1997.
High coordination lattice models of protein structure, dynamics and thermodynamics. Acta biochimica Polonica. 44(3):389-422. PDF. 1997.
Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction. Folding & design. 2(4):247-59. PDF. 1997.
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. Journal of Computational Chemistry. 18(1):80-85. PDF. 1997.
Method for low resolution prediction of small protein tertiary structure. Pacific Symposium on Biocomputing 1997. :316-327. PDF. 1997.
Monte Carlo Lattice Dynamics and the Prediction of Protein Folds. Computer Simulations of Biomolecular Systems. 3:395-429. PDF. 1997.
A Monte Carlo model of fd and Pf1 coat proteins in membranes. Chemtracts. 10:242-245. PDF. 1997.
On the origin of the cooperativity of protein folding: implications from model simulations.. Proteins. 26(3):271-87. PDF. 1996.
Folding simulations and computer redesign of protein A three-helix bundle motifs. Proteins. 25(3):286-99. PDF. 1996.
Method for predicting the state of association of discretized protein models. Application to leucine zippers.. Biochemistry. 35(3):955-67. PDF. 1996.
Does a backwardly read protein sequence have a unique native state? Protein engineering. 9(1):5-14. PDF. 1996.
Predicting leucine zipper structures from sequence. Protein engineering. 9(8):657-62. PDF. 1996.
An algorithm for prediction of structural elements in small proteins. Pacific Symposium on Biocomputing (PSB-96). :446-460. PDF. 1996.
Lattice Models of Protein Folding. Dynamics and Thermodynamics. :202.. 1996.
Monte Carlo Models of Spontaneous Insertion of Peptides into Lipid Membranes. Membrane Structures & Dynamics. :535-554. PDF. 1996.
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets Protein science : a publication of the Protein Society. 4(10):2107-17. PDF. 1995.
A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes. Biophysical journal. 69(4):1382-6. PDF. 1995.
Spontaneous translocation of a polymer across a curved membrane. Physical review letters. 74(11):2142-2145. PDF. 1995.
Neural network system for the evaluation of side-chain packing in protein structures. Protein engineering. 8(3):225-36. PDF. 1995.
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. Journal of molecular biology. 251(3):448-67. PDF. 1995.
A reduced model of short range interactions in polypeptide chains. The Journal of Chemical Physics. 103(10):4312. PDF. 1995.
A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations. The Journal of Chemical Physics. 102(15):6189. PDF. 1995.