PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. Journal of Chemical Information and Modeling. 55(8):1757-1770. PDF. 2015.
Ab initio folding of proteins using restraints derived from evolutionary information. Proteins. Suppl 3:177-85. PDF. 1999.
Ab Initio modeling. :137-162.. 2005.
Ab initio modeling of small proteins by iterative TASSER simulations. BMC biology. 5:17. PDF. 2007.
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.
Ab initio protein structure prediction using chunk-TASSER. Biophysical journal. 93(5):1510-8. PDF. 2007.
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.. Protein science : a publication of the Protein Society. 13(2):400-11.. 2004.
Active site recognition in silico. Structure-function relation in proteins. 1:105-127.. 2009.
Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges. Structure. 22(8):1120-1139. PDF. 2014.
Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Environmental microbiology. 9(12):3122-33. PDF. 2007.
An algorithm for prediction of structural elements in small proteins. Pacific Symposium on Biocomputing (PSB-96). :446-460. PDF. 1996.
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. Journal of Computational Chemistry. 18(1):80-85. PDF. 1997.
All-atom ab initio folding of a diverse set of proteins. Structure (London, England : 1993). 15(1):53-63. PDF. 2007.
Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila. FEBS Journal. 281(6):1613-1628. PDF. 2014.
Analysis of TASSER-based CASP7 protein structure prediction results. Proteins. 69 Suppl 8:90-7. PDF. 2007.
APoc: large-scale identification of similar protein pockets. Bioinformatics. 29(5):597-604. PDF. 2013.
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.
Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nature biotechnology. 16(8):753-6. PDF. 1998.
Application of reduced models to protein structure prediction. Computational Molecular Biology. 8:397-440. PDF. 1999.
Application of sparse NMR restraints to large-scale protein structure prediction. Biophysical journal. 87(2):1241-8. PDF. 2004.
Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers. 70(4):575-84. PDF. 2003.
Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current opinion in structural biology. 23(2):191-7. PDF. 2013.
Are protein-protein interfaces special regions on a protein’s surface? The Journal of Chemical Physics. 143(24):243149. PDF. 2015.
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.
Assembly of anthrax toxin pore: Lethal-factor complexes into lipid nanodiscs. Protein Science. 22(4):492-501.. 2013.
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins. 32(4):475-94. PDF. 1998.
Assessment of programs for ligand binding affinity prediction. Journal of computational chemistry. 29(8):1316-31. PDF. 2008.
Asymmetric processing of a substrate protein in sequential allosteric cycles of AAA+ nanomachines. The Journal of Chemical Physics. 139(12):121921.. 2013.
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins: Structure, Function, and Bioinformatics. 79(S10):147-160.. 2011.
Automated structure prediction of weakly homologous proteins on a genomic scale. Proceedings of the National Academy of Sciences of the United States of America. 101(20):7594-9. PDF Supplementary Data. 2004.
Benchmarking of dimeric threading and structure refinement. Proteins. 63(3):457-65. PDF. 2006.
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophysical journal. 95(4):1956-64. PDF. 2008.
Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy. Proceedings of the Royal Society B: Biological Sciences. 278(1714):1930-1935.. 2011.
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Research.. 2012.
BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics (Oxford, England). 17(5):468-78. PDF. 2001.
Biophysical and structural considerations for protein sequence evolution. BMC Evolutionary Biology. 11(1):361.. 2011.
Bound Ligand Conformer Revealed by Flexible Structure Alignment in Absence of Crystal Structures: Indirect Drug Design Probed for HIV-1 Protease Inhibitors. Journal of Chemical Theory and Computation. 5(3):659-673.. 2009.
Brownian dynamics simulation of macromolecule diffusion in a protocell. Proceedings of the International Conference of the Quantum Bio-Informatics IV. 28:413-426. PDF. 2011.
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking Journal of computational chemistry. 28(12):2059-66. PDF Supplementary Data. 2007.