MSITE: a new computational tool for comparison of homological proteins in holo formThe Journal of Steroid Biochemistry and Molecular Biology 121, 34-42, 2010.
Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained modelsBMC Structural Biology 8, 36, 2008.
Fast and accurate methods for predicting short-range constraints in protein modelsJournal of Computer-Aided Molecular Design 22, 783–8, 2008.
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinatesJournal of Computational Chemistry 28, 1593–7, 2007.
Comparative modeling without implicit sequence alignmentsBioinformatics (Oxford, England) 23, 2522–7, 2007.
Protein structure prediction: combining de novo modeling with sparse experimental dataJournal of Computational Chemistry 28, 1668–76, 2007.
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of modelsProteins 61 Suppl. 7, 84–90, 2005.
A minimal proteinlike lattice model: an alpha-helix motifThe Journal of Chemical Physics 122, 214915, 2005.
A new approach to prediction of short-range conformational propensities in proteinsBioinformatics (Oxford, England) 21, 981–987, 2005.
Solvent polarity and hydrogen-bonding effects on the nitrogen NMR shieldings of N-nitrosamines and DFT calculations of the shieldings of C-, N-, and O-nitroso systemsJournal of Magnetic Resonance 164, 212-9, 2003.
TOUCHSTONE II: a new approach to ab initio protein structure predictionBiophysical Journal 85, 1145–64, 2003.
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeProceedings of the National Academy of Sciences of the United States of America 99, 5993–5998, 2002.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsProceedings of the National Academy of Sciences of the United States of America 98, 10125–30, 2001.