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On the importance of COmposite Protein multiple LIGand (COLIG) Interactions in Protein Pockets. Journal of Computational Chemistry.. Submitted.
Why is there a glass ceiling for threading-based structure prediction methods? Journal of Physical Chemistry B.. Submitted.
Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules. The Journal of Chemical Physics. 145:100901. PDF. In Press.
Repurposing FDA-approved drugs for anti-aging therapies. Biogerontology. PDF. In Press.
How special is the biochemical function of native proteins? F1000Research. 5:207. PDF. 2016.
Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway. Bioorganic & Medicinal Chemistry. 24(19):4750-4758. PDF. 2016.
Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase. Biochemical Journal. 473(14):2165-2177. PDF. 2016.
A knowledge-based approach for predicting gene-disease associations. Bioinformatics. :btw358. PDF. 2016.
Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Scientific Reports. 5:11090. PDF. 2015.
LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. Bioinformatics (Oxford, England). 31(4):539-44. PDF. 2015.
Metabolomics identifies the intersection of phosphoethanolamine with menaquinone-triggered apoptosis in an in vitro model of leukemia. Mol. BioSyst.. 11(9):2406-2416. PDF. 2015.
Are protein-protein interfaces special regions on a protein’s surface? The Journal of Chemical Physics. 143(24):243149. PDF. 2015.
Effects of confinement on models of intracellular macromolecular dynamics. Proceedings of the National Academy of Sciences. 112(48):14846-14851. PDF. 2015.
PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. Journal of Chemical Information and Modeling. 55(8):1757-1770. PDF. 2015.
GS-align for glycan structure alignment and similarity measurement. Bioinformatics. 31(16):2653-2659. PDF. 2015.
Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. Structure. 23(7):1362-1369. PDF. 2015.
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. Bioorganic & Medicinal Chemistry Letters. 25:1163-1170. PDF. 2015.
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. Journal of Cheminformatics. 6(1):16. PDF. 2014.
Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models. PLoS Computational Biology. 10(12):e1003990. PDF. 2014.
Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges. Structure. 22(8):1120-1139. PDF. 2014.
On the Role of Physics and Evolution in Dictating Protein Structure and Function. Israel Journal of Chemistry. 54(8-9):1176-1188. PDF. 2014.
WeFold: A Coopetition for Protein Structure Prediction. Proteins: Structure, Function, and Bioinformatics. :n/a-n/a. PDF. 2014.
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Computational Biology. 9(3):e1002946. PDF. 2013.
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.
Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biology. 11(1):44. PDF. 2013.
A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. PLoS Computational Biology. 9(10):e1003302. PDF. 2013.
On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation. Biophysical Journal. 104(1):96-105. PDF. 2013.
Interplay of physics and evolution in the likely origin of protein biochemical function. Proceedings of the National Academy of Sciences. 110(23):9344-9349. PDF. 2013.
APoc: large-scale identification of similar protein pockets. Bioinformatics. 29(5):597-604. PDF. 2013.
FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. Journal of Chemical Information and Modeling. 53(1):230-240. PDF. 2013.
Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations. Journal of Chemical Physics. 139:121922-1. PDF. 2013.
Importance of excluded volume and hydrodynamic interactions on macromolecular diffusion in vivo. International Conference of the Quantum Bio-Informatics IV. 30:378-387. PDF. 2013.
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics. 28(20):2687-2688. PDF. 2012.
Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. The Journal of Chemical Physics. 137:064106. PDF. 2012.
FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs. Molecular Pharmaceutics. 9(6):1775-1784. PDF. 2012.
Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures. The Journal of Physical Chemistry B. 116(23):6654-6664. PDF. 2012.
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proceedings of the National Academy of Sciences. 109(10):3784-3789. PDF. 2012.
Template-based protein structure modeling using TASSERVMT. Proteins: Structure, Function, and Bioinformatics. 80(2):352-361. PDF. 2012.
Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment. Structure. 19(8):1108-1126. PDF. 2011.
GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction. Biophysical Journal. 101(8):2043-2052. PDF. 2011.
New benchmark metrics for protein-protein docking methods. Proteins: Structure, Function, and Bioinformatics. 79(5):1623-1634. PDF. 2011.
FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins: Structure, Function, and Bioinformatics. 79(3):735-751. PDF. 2011.
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. Journal of Structural Biology. 173(3):558-569. PDF. 2011.