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Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48(2):192-201. PDF. 2002.
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proceedings of the National Academy of Sciences of the United States of America. 99(9):5993-8. PDF. 2002.
Computer simulations of protein folding with a small number of distance restraints. Acta biochimica Polonica. 49(3):683-92. PDF. 2002.
Universal similarity measure for comparing protein structures. Biopolymers. 59(5):305-9. PDF. 2001.
Enhanced functional annotation of protein sequences via the use of structural descriptors. Journal of structural biology. 134(2-3):232-45. PDF. 2001.
BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics (Oxford, England). 17(5):468-78. PDF. 2001.
Defrosting the frozen approximation: PROSPECTOR--a new approach to threading. Proteins. 42(3):319-31. PDF. 2001.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proceedings of the National Academy of Sciences of the United States of America. 98(18):10125-30. PDF. 2001.
A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 44(3):223-32. PDF. 2001.
Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures. The Journal of Chemical Physics. 115(11):5027. PDF. 2001.
Finding the needle in a haystack: educing native folds from ambiguousab initio protein structure predictions. Journal of Computational Chemistry. 22(3):339-353. PDF. 2001.
A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics. Journal of Computational Physics. 115:1569-1574. PDF. 2001.
Sequence evolution and the mechanism of protein folding. Biophysical journal. 79(4):1787-99. PDF. 2000.
Structural genomics and its importance for gene function analysis. Nature biotechnology. 18(3):283-7. PDF. 2000.
Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins. 38(1):3-16. PDF. 2000.
From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends in biotechnology. 18(1):34-9. PDF. 2000.
Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures. The Journal of Chemical Physics. 113(12):5065. PDF. 2000.
Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model. Macromolecular Theory and Simulations. 9(8):523-533. PDF. 2000.
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1. Journal of the American Chemical Society. 122(35):8392-8402. PDF. 2000.
Structure of proteins: New approach to molecular modeling. Polish J. Chem. 75:587-599. PDF. 2000.
Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. The FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 13(13):1866-74. PDF. 1999.
From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein science : a publication of the Protein Society. 8(5):1104-15. PDF. 1999.
De novo simulations of the folding thermodynamics of the GCN4 leucine zipper. Biophysical journal. 77(1):54-69. PDF. 1999.
A method for the improvement of threading-based protein models. Proteins. 37(4):592-610. PDF. 1999.
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. Biophysical journal. 77(6):2942-52. PDF. 1999.
Ab initio folding of proteins using restraints derived from evolutionary information. Proteins. Suppl 3:177-85. PDF. 1999.
Supramolecular self-assembly: molecular dynamics modeling of polyhedral shell formation. Computer Physics Communications. 121-122:231-235. PDF. 1999.
Application of reduced models to protein structure prediction. Computational Molecular Biology. 8:397-440. PDF. 1999.
Correlation between knowledge‐based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper. Proteins: Structure, Function, and Genetics. 35(4):447-452. PDF. 1999.
De novo predictions of the quaternary structure of leucine zippers and other coiled coils. International Journal of Quantum Chemistry. 75(3):165-176. PDF. 1999.
Derivation and testing residue-residue mean force potentials for use in protein structure recognition. Protein Structure Prediction Methods and Protocols. :155-174. PDF. 1999.
The role of computational biology in the genomics revolution. National Research Council’s Chemical Sciences Roundtable Workshop on the Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology. PDF. 1999.
Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. Journal of molecular biology. 281(5):949-68. PDF. 1998.
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins. 32(4):475-94. PDF. 1998.
Reduced protein models and their application to the protein folding problem.. Journal of biomolecular structure & dynamics. 16(2):381-96. PDF. 1998.
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.