IBBR Publications

Yu W, Lakkaraju SKaushik, E Raman P, Fang L, Mackerell AD. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J Chem Inf Model. 2015 ;55(2):407-20.

Purushottamachar P, Patel JB, Gediya LK, Clement OO, Njar VCO. First chemical feature-based pharmacophore modeling of potent retinoidal retinoic acid metabolism blocking agents (RAMBAs): identification of novel RAMBA scaffolds. Eur J Med Chem. 2012 ;47(1):412-23.

Oashi T, Ringer AL, E Raman P, Mackerell AD. Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness. J Chem Inf Model. 2011 ;51(1):148-58.

Liao W-L, Heo G-Y, Dodder NG, Reem RE, Mast N, Huang S, Dipatre PLuigi, Turko IV, Pikuleva IA. Quantification of cholesterol-metabolizing P450s CYP27A1 and CYP46A1 in neural tissues reveals a lack of enzyme-product correlations in human retina but not human brain. J Proteome Res. 2011 ;10(1):241-8.

Lowenthal MS, Gasca-Aragon H, Schiel JE, Dodder NG, Bunk DM. A quantitative LC-MS/MS method for comparative analysis of capture-antibody affinity toward protein antigens. J Chromatogr B Analyt Technol Biomed Life Sci. 2011 ;879(26):2726-32.

Fernandes R, Luo X, Tsao C-Y, Payne GF, Ghodssi R, Rubloff GW, Bentley WE. Biological nanofactories facilitate spatially selective capture and manipulation of quorum sensing bacteria in a bioMEMS device. Lab Chip. 2010 ;10(9):1128-34.

Hatcher E, Guvench O, Mackerell AD. CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B. 2009 ;113(37):12466-76.

Guvench O, Mackerell AD. Computational fragment-based binding site identification by ligand competitive saturation. PLoS Comput Biol. 2009 ;5(7):e1000435.

Shen Y, Delaglio F, Cornilescu G, Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR. 2009 ;44(4):213-23.

Bastas G, Sompuram SR, Pierce BG, Vani K, Bogen SA. Bioinformatic requirements for protein database searching using predicted epitopes from disease-associated antibodies. Mol Cell Proteomics. 2008 ;7(2):247-56.

Zhong S, Chen X, Zhu X, Dziegielewska B, Bachman KE, Ellenberger T, Ballin JD, Wilson GM, Tomkinson AE, Mackerell AD. Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem. 2008 ;51(15):4553-62.

Yan Y, Moult J. Detection of operons. Proteins. 2006 ;64(3):615-28.

Unger R, Moult J. Towards computing with proteins. Proteins. 2006 ;63(1):53-64.

Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins. 2005 ;61 Suppl 7:225-36.

Mintseris J, Wiehe K, Pierce BG, Anderson R, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins. 2005 ;60(2):214-6.

Wu Z, Delaglio F, Wyatt K, Wistow G, Bax A. Solution structure of (gamma)S-crystallin by molecular fragment replacement NMR. Protein Sci. 2005 ;14(12):3101-14.

Yampolsky LY, Stoltzfus A. Untangling the effects of codon mutation and amino acid exchangeability. Pac Symp Biocomput. 2005 :433-44.

Wiehe K, Pierce BG, Mintseris J, Tong WWei, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 2005 ;60(2):207-13.

Grishaev A, Bax A. An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. J Am Chem Soc. 2004 ;126(23):7281-92.

Gaponenko V, Sarma SP, Altieri AS, Horita DA, Li J, R Byrd A. Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints. J Biomol NMR. 2004 ;28(3):205-12.

DeWeese-Scott C, Moult J. Molecular modeling of protein function regions. Proteins. 2004 ;55(4):942-61.

Wu C, Njar VCO, Brodie A, Borenstein M, Nnane I. Quantification of a novel retinoic acid metabolism inhibitor, 4-(1H-imidazol-1-yl)retinoic acid (VN/14-1RA) and other retinoids in rat plasma by liquid chromatography with diode-array detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 ;810(2):203-8.

Venclovas C, Zemla A, Fidelis K, Moult J. Assessment of progress over the CASP experiments. Proteins. 2003 ;53 Suppl 6:585-95.

Janin J, Henrick K, Moult J, Eyck LTen, Sternberg MJE, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 2003 ;52(1):2-9.

Wu C-F, Valdes JJ, Bentley WE, Sekowski JW. DNA microarray for discrimination between pathogenic 0157:H7 EDL933 and non-pathogenic Escherichia coli strains. Biosens Bioelectron. 2003 ;19(1):1-8.