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1. Yang, B., Wright, J., Eldefrawi, M.E., Poi, S.,and MacKerell Jr., A.D., "Conformational, aqueous solvation and pKa contributions to the binding of cocaine, WIN and a WIN vinyl analog," Journal of the American Chemical Society, 116:8722-8732, 1994.


2. Li, Y., MacKerell, Jr., A.D., Egorin, M.J., Ballesteros, M.F., Rosen, D.M., Wu, Y.-Y., Blamble, D.A. and Callery, P.S., "Structure-Function Relationships of Polyamine Transport Inhibitors in L1210 Murine Leukemia Cells," Cancer Investigation, 57: 234-239, 1997.


3. Lieske, S., Yang, B., Eldefrawi, M.E. and MacKerell Jr., A.D., and Wright, J., "(-)3b-Substituted Ecgonine Methyl Esters as Inhibitors for Cocaine Binding and Dopamine Uptake.," Journal of Medicinal Chemistry, 41: 864-876, 1998.


4. Chen, I.J., Neamati, N., Nicklaus, M.C., Orr, A., Anderson, L., Barchi, Jr., J.J., Kelley, J.A., Pommier, Y., and MacKerell, Jr. A.D., "Identification of HIV-1 Integrase Inhibitors via Three-Dimensional Database Searching using ASV and HIV-1 Integrases as Targets," Bioorganic & Medicinal Chemistry, 8: 2385- 2389, 2000.


5. Chen, I-J., Neamati, N. and MacKerell, Jr. A.D., "Structure-Based Inhibitor Design Targeting HIV-1 Integrase," Current Drug Targets - Infectious Disorders, 2: 217-234, 2002.


6. Pan, Y., Huang, N., Cho, S. and A. D. MacKerell, Jr., "Consideration of molecular weight during compound selection in virtual database screening," Journal of Chemical Information and Computer Science, 43: 267-272, 2003.


7. Chen, W., Wu, H,. Bernard, D., Metcalf, M.D., Deschamps, J., Flippen-Anderson, J., MacKerell, Jr,, A.D. and Coop, A., "Rearrangement of 5- Trimethylsilylthebaine on Treatment with L-Selectride: An Efficient Synthesis of (+)-Bractazonine," Journal of Organic Chemistry, 68: 1929-1932, 2003.


8. Bernard, D., A. Coop, A. and MacKerell, Jr., A.D., "2D Conformationally Sampled Pharmacophore: A Novel Approach to Ligand Based Pharmacophore Development Applied to δ Opioid Agonists and Antagonists,"Journal of the American Chemical Society. 125: 3103-3107, 2003.


9. Rosen, G.M, Beselman, A., Tsai, P., Pou, S., Mailer, C. Ichikawa, K,. Robinson, B.H., Nielsen, R., Halpern, H. and MacKerell, A.D. Jr., "Influence of Structure on the EPR Spectrum of Spin Trapped Adducts of 5,5-Dimethyl-1-Pyrroline-N- Oxide," Journal of Organic Chemistry, 69: 1321-1330, 2004.


10. Macias, A., Hernandez, R.J., Mehta, A.K., MacKerell, A.D., Jr., Ticku, M.K. and Coop, A., "3-Chloropropanoic acid (UMB66): a ligand for the gamma- hydroxybutyric acid receptor lacking a 4-hydroxyl group,"Bioorganic & Medicinal Chemistry, 12: 1643-1647, 2004.


11. Huang, N., Nagarsekar, A., Xia, G., Hayashi, J., MacKerell, A.D., Jr., "Identification of Non-phosphate containing Small Molecular Weight Inhibitors of the Tyrosine Kinase p56 LCK SH2 Domain via In silico Screening against the pY+3 site," Journal of Medicinal Chemistry, 47: 3502-3511, 2004.


12. MacKerell, A.D., Jr., "Empirical Force Fields for Biological Macromolecules: Overview and Issues," Journal of Computational Chemistry, 25: 1584-1604, 2004.


13. Markowitz, J., Chen, I., Gitti, R., Baldisseri, D. M., Pan, Y., Udan, R., Carrier, F., MacKerell, A. D., Jr., Weber, D. J., "Identification and Characterization of Small Molecule Inhibitors of the Calcium-Dependent S100B-p53 Tumor Suppressor Interaction," Journal of Medicinal Chemistry, 47; 5085-5093, 2004.


14. Wu, H., D. Bernard, W. Chen, G.D. Strahan, J.R. Deschamps, D.A. Parrish, J.W. Lewis, Al.D. MacKerell, Jr., and A. Coop, "Functionalization of the 6,14-bridge of the orvinols. 2. Preparation of 18- and 19-hydroxyl substituted thevinols and their treatment with benzyl bromide. Submitted to the Journal of Organic Chemistry, 70: 1907-1910, 2005.


15. Boresch, S., Leitgeb, M., Beselman, A., MacKerell, A.D., Jr., "Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives" Journal of the American Chemical Society, 127; 4640-4648, 2005.


16. H. Wu, L. N. Thatcher, D. Bernard, D. A. Parrish, J. R. Deschamps, K. C. Rice, A. D. MacKerell Jr., A. Coop., "The Position of Coordination of the Lithium Ion Determines the Regioselectivity of Demethylations of 3,4-Dimethoxymorphinans with L-Selectride," Organic Letters, 7, 2531-2534, 2005.


17. Bernard, D., Coop, A. and MacKerell, Jr., A.D. "Computer-Aided Drug Design: Structure-Activity Relationships of Delta Opioid Ligands," Drug Design Reviews, 2005, 2: 277-291.


18. Hancock, C.N., Macias, A. Lee, E.K., Yu, S.Y., MacKerell, Jr., A.D. and Shapiro, P., "Identification of novel extracellular signal-regulated kinase (ERK) docking domain inhibitors," Journal of Medicinal Chemistry, 2005, 48; 4586-4595.


19. Markowitz, J., MacKerell, A. D., Jr., Carrier, F., Charpentier, T.H., Weber, D. J., "Design of Inhibitors of S100B," Current Topics in Medicinal Chemistry, 2005, 5: 1093-1108.


20. Bernard, D., Coop, A., MacKerell, A. D., Jr., "Conformationally Sampled Pharmacophore for Peptidic δ-Opioid Ligands," Journal of Medicinal Chemistry, 2005, 48: 7773-7780.


21. Macias, A.T., Mia, M.Y., Xia, G., Hayashi, J. and MacKerell, Jr., A.D., "Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56lck," Journal of Chemical Information and Modeling, 2005, 45: 1759-1766.


22. Hancock, C.N., Macias, A., MacKerell, Jr. A.D., and Shapiro, P., "Mitogen Activated Protein (MAP) Kinases: Development of ATP and Non-ATP Dependent Inhibitors," Medicinal Chemistry, 2006, 2, 213-222.


23. Chen, I.-J., Taneja, R., Yin, D., Seo, P.R., Young, D., MacKerell, Jr., A.D., and Polli, J.E., "Chemical Substituent Effect on Pyridine Permeability and Mechanistic Insights from Computational Molecular Descriptors," Molecular Pharmaceutics, 3:745-755, 2006.


24. Zhong, S., Macias, A.T., MacKerell, Jr., A.D. "Computational identification of the inhibitors of protein-protein interactions," Current Topics in Medicinal Chemistry, 7, 63-82, 2007.


25. Chen, F., Hancock, C.N., Macias, A.T., Joh, J., Still, K., Zhong, S., MacKerell, Jr., A.D. Shapiro, P.S., "Characterization of ATP independent ERK inhibitors identified through in silico analysis of the active ERK2 structure," Bioorganic and Medicinal Chemistry Letters, 16:6281-627, 2006.


26. Markowitz, J., MacKerell, Jr., A.D., and Weber, D.J. "A search for inhibitors of S100B, a member of the S100 family of calcium-binding proteins," Mini-Reviews in Medicinal Chemistry, 7: 609-616, 2007, PMID: 17584159.


27. Bernard, D., Coop, A. and MacKerell, Jr., A.D. "Quantitative Conformationally Sampled Pharmacophore for d Opioid Ligands: Reevaluation of Hydrophobic Moieties Essential for Biological Activity," Journal of Medicinal Chemistry, 50: 1799-1809, 2007.


28. Furci, L.M., Lopes, P., Eakanunkul, S., Zhong, S., MacKerell, A.D., Jr., Wilks, A., "Inhibition of the Bacterial Heme Oxygenases from Pseudomonas aeruginosa (pa-HO) and Neisseria meningitidis (nm-HO): A Novel Antimicrobial Target," Journal of Medicinal Chemistry, 50: 3804-3813, 2007.


29. Zhong, S. and MacKerell, Jr., A.D. "Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces," Journal of Chemical Information and Modeling, 47; 2303-2315, 2007, PMID: 17900106.


30. Chen, X., Zhong S., Zhu, X., Dziegielewska, B., Ellenberger, T., Wilson, G.M, Bachman, K., MacKerell, Jr., A.D. and Tomkinson, A.E., "Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair," Cancer Research, 68: 3169-3177, 2008, PMID: 18451142.


31. Yu, W.-M., Guvench, O., MacKerell, Jr., A.D., and Qu. C.-K. "Identification of small molecular weight inhibitors of SHP-2 tyrosine phosphatase via in silico screening combined with experimental assay." Journal of Medicinal Chemistry, 51: 7396-7404, 2008. PMID: 19007293.


32. Zhong, S. and MacKerell, Jr., A.D. "Pose Scaling: Geometrical Assessment of Ligand Binding Poses," Journal of Theoretical and Computational Chemistry, 7: 833–852, 2008.


33. Acharya, C., Seo, P.R., Polli, J.E. MacKerell, Jr., A.D. "Computational Model for Predicting Chemical Substituent Effects on Passive Drug Permeability across Parallel Artificial Membranes" Molecular Pharmaceutics, 5, 818–828, 2008, DOI: 10.1021/mp800035h, PMID: 18710255.


34. Zhong, S., Chen, X., Zhu, X., Dziegielewska, B., Bachman, K.E., Ellenberger, T., Ballin, J.D., Wilson, G.M., Tomkinson, A.E. and MacKerell, Jr., A.D., "Identification and Validation of Human DNA Ligase Inhibitors using Computer- Aided Drug Design," Journal of Medicinal Chemistry, 51; 4553-4562, 2008, PMID: 18630893, DOI: 10.1021/jm8001668.


35. Charpentier, T.H., Wilder, P.T., Liriano, M.A., Varney, K.M., Pozharski, E, MacKerell, Jr., A.D., Coop, A., Toth, E.A., Weber, D.J., "Divalent metal ion complexes of S100B in the absence and presence of pentamidine," Journal of Molecular Biology, 382:56-73, 2008, PMID: 18602402.


36. Chen, F., MacKerell, Jr., A.D., Luo, Y. and Shapiro, P. "Using Caenorhabditis elegans as a Model Organism for Evaluating Extracellular Signal-Regulated Kinase Docking Domain Inhibitors," Journal of Cell Communication and Signaling, 2:81-92. 2008 PMID: 19105050.


37. Matthews, M.M., Weber, D.J., Shapiro, P.S., Coop, A., and MacKerell, Jr., A.D. "Inhibition of protein-protein interactions with low molecular weight compounds," Current Trends in Medicinal Chemistry, 5, 21-32, 2008, NIHMSID197598.


38. Guvench, O., and MacKerell, Jr., A.D. "Computational evaluation of protein – small molecule binding," Current Opinion in Structural Biology, 19:56–61, 2009. PMC2671234.


39. González, P.M., Acharya, C., MacKerell, Jr., A.D. and Polli, J.E., "Inhibition Requirements of the human Apical Sodium-dependent Bile acid Transporter (hASBT) using Aminopiperidine Conjugates of glutamyl-Bile Acids," Pharmaceutical Research, 26: 1665-1678, 2009.


40. Guvench, O., and MacKerell, Jr., A.D. "Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation," PLoS Computational Biology, 5: e1000435, 2009, PMC2700966.


41. Vanommeslaeghe, K. Hatcher, E., Acharya, C., Kundu, S. Zhong, S., Shim, J., E. Darian, E., Guvench, O., Lopes, P., Vorobyov, I., MacKerell, A.D., Jr., "CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields," Journal of Computational Chemistry, 31: 671-90, 2010, NIHMSID 196732, PMC2888302.


42. Charpentier, T.H., Wilder, P.T., Liriano, M.A., Varney, K.M., Zhong, S., Coop, A., Pozharski, E., MacKerell, Jr., A.D., Toth, E.A., Weber, D.J. "Small Molecules Bound to Unique Sites in the Target Protein Binding Cleft of Calcium- Bound S100B As Characterized by Nuclear Magnetic Resonance and X-ray Crystallography," Biochemistry, In Press, 2009, PMID: 19469484.


43. Cerchietti, L.C., Ghetu, A.F., Zhu, X., Da Silva, G.F., Zhong, S., Matthews, M., Bunting, K., Polo, J.M., Farès, C., Arrowsmith, C.H., Yang, S.N., Garcia, M., Coop, A., MacKerell, A.D., Jr. , Privé, G.G., Melnick, A. "A small molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo," Cancer Cell, 17, 400– 411, 2010, PMC2858395.


44. Rais, R., Acharya, C., Tririya, G, MacKerell, A.D., Jr., and Polli, J. "Molecular Switch Controlling the Binding of Anionic Bile Acid Conjugates to hASBT," Journal of Medicinal Chemistry, 53: 4749-4760, 2010, PMC2891776.


45. Huang, N., Kolhatkar, R., Eyobo, Y., Sorci, L, Osterman, A.L, MacKerell, A.D., Jr., and Zhang, H., "Structures of bacterial NaMN adenylyltransferase in complex with inhibitors: implication for structure based drug design and improvement," Journal of Medicinal Chemistry, 53: 5229-5239, 2010, PMC2915899.


46. Wilder, P.T., Charpentier, T.H., Liriano, M.A., Gianni, K., Varney, K.M., Pozharski, E., Coop, A., Toth, E.A., MacKerell, A.D., Jr., Weber, D.J. "In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction," International Journal of High Throughput Screening. 1:109–126, 2010, PMC2995924.


47. Semenyuk, A., Darian, E., Liu, J., Majumdar, A., Cuenoud, B., Miller, P., MacKerell, A.D., Jr., Seidman, M. "Targeting of an interrupted Polypurine:Polypyrimidine sequence in a Triplex forming oligonucleotide containing a novel base analog," Biochemistry, 49: 7867-7878, 2010, PMC2935506.


48. Acharya, C., Polli, J., Coop, A. and, MacKerell, A.D., Jr., "Recent Advances in Ligand-Based Drug Design: Relevance and Utility of the Conformationally Sampled Pharmacophore Approach," Current Computer-Aided Drug Design, 7:10-22, 2011, NIHMSID #230044.


49. Rais, R., Acharya, C., MacKerell, A.D., Jr., Polli, J., "Structural Determinants for Transport Across the Intestinal Bile Acid Transporter Using C-24 Bile Acid Conjugates," Molecular Pharmaceutics, 7:2240-2254, 2010, PMC2997912.


50. Oashi, T., Ringer, A.L., Raman, E.P., and MacKerell, A.D., Jr., "Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness," Journal of Chemical Information and Modeling, 51:148-158, 2011, PMC3160130.


51. Yap, J.L., Workikar, S., MacKerell, A.D., Jr., Shapiro, P., and Fletcher, S. "Small-Molecule Inhibitors of the ERK Signalling Pathway: Towards Novel Anticancer Therapeutics," ChemMedChem, 6: 38-48, 2011.


52. Velvadapu, V., Paul, T., Wagh, B., Klepacki, D., Guvench, O., MacKerell, A.D., Jr., and Andrade, R.B., "Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Telithromycin," ACS Medicinal Chemistry Letters, 2: 68– 72, 2011, PMC3105755.


53. Boston, S.R., Deshmukh, R., Strome, S., Priyakumar, U.D., MacKerell, A.D., Jr., and Paul Shapiro, P. "Characterization of ERK Docking Domain Inhibitors that Induce Apoptosis by Targeting Rsk-1 and Caspase-9," BMC Cancer, 11: 7, 2011, PMC3025971.


54. Darian, E., Guvench, O. Yu, B., Qu, C.-K., and MacKerell, A.D., Jr., "Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase," Proteins: Structure, Function and Bioinformatics, 79: 1573–1588, 2011, PMC3076527.


55. Busby, B., Oashi, T., Willis, C.D., Borzok, M.A., Kontrogianni-Konstantopoulos, A., MacKerell, A.D., Jr., and Bloch, B.J. "Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies," Journal of Molecular Biology, 408:321-334, 2011.


56. Raman, E.P., Yu, W., Guvench, O. and MacKerell, A.D., Jr., "Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations," Journal of Chemical Information and Modeling, 51, 877-890, 2011, PMC3090225.


57. Shim, J., and MacKerell, A.D., Jr., "Computational ligand-based rational design: Role of conformational sampling and force fields in model development," Med. Chem. Commun., 2: 356-370, 2011, DOI: 10.1039/c1md00044f, PMC3123535.


58. Shim, J., Coop, A. and Alexander D. MacKerell, A.D., Jr. "Consensus 3D Model of μ-Opioid Receptor Ligand Efficacy based on a Quantitative Conformationally Sampled Pharmacophore," Journal of Physical Chemistry B, 115: 7487-7496, 2011, PMC3113728.


59. Kolhatkar, V., Diao, L., Acharya, C., MacKerell, A.D., Jr., Polli, J. "Identification of novel non-steroidal compounds as substrates or inhibitors of hASBT," Journal of Pharmaceutical Sciences, 101: 116-126, 2012, DOI: 10.1002/jps.22728.


60. Fribourg, M., Moreno, J.L., Provasi, D., Holloway, T., Mahajan, R., Park, G., Baki, L., Adney, S.K., Hatcher, C., Ruta, J.D., Albizu, L., Li, Z., Shim, J., Fabiato, A., MacKerell, A.D., Jr., Brezina, V., Sealfon, S.C., Filizola, M., González-Maeso, J. and Logothetis, D.E., "Decoding the signalling of a GPCR heteromeric complex reveals the mechanism of action of antipsychotic drugs," Cell, 147: 1011-1023, 2011.


61. Xu, Z., Chen, Y.-W., Battu, A., Wilder, P., Weber, D., Yu, W., MacKerell, A.D., Jr. Chen, L.-M., Chai, K., Johnson, M., Lin, C.-Y., "Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade," Journal of Medicinal Chemistry, 54: 7567-7578, 2011, PMC3214968.


62. Underwood, K., D'Souza, D., Mochin-Peters, M., Pierce, A., Kommineni, S., Choe, M., Bennett, J., Gnatt, A., Habtemariam, B., MacKerell, A., and Passaniti, A. "Regulation of RUNX2 transcription factor-DNA interactions and cell proliferation by Vitamin D3 (cholecalciferol) prohormone activity," Journal of Bone and Mineral Research, 27: 913-925, 2012, 10.1002/jbmr.1504.


63. Yap, J.L., Cao, X., Vanommeslaeghe, A., Jung, K.-Y., Wilder, P.T., Anjan Nan, A., Hom, K., MacKerell, A.D., Jr., Smythe, W.R., and Fletcher, S.,"Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors," Organic and Biomolecular Chemistry, 16: 2269-2283, 2012, DOI: 10.1039/c2ob07125h.


64. Velvadapu, V., Glassford, I., Lee, M., Paul, T., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B., "Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin," ACS Medicinal Chemistry Letters, 3: 211-215, 2012, PMC3374412.


65. González, P.M., Hussainzada, N., Swaan, P.W., MacKerell Jr., A.D., and Polli, J.E., "Putative irreversible inhibitors of the human sodium-dependent bile acid transporter (hASBT; SLC10A2) support the role of transmembrane domain 7 in substrate binding/translocation," Pharmaceutical Research, 29: 1821-1831, 2012, doi: 10.1007/s11095-012-0706-8.


66. Raman, E.P., Vanommeslaeghe, K. and MacKerell Jr., A.D., "Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations," Journal of Chemical Theory and Computation, 8: 3513-3525, 2012, PMC3490637, doi: 10.1021/ct300088r.


67. Foster, T.J., MacKerell Jr., A.D. and Guvench, O. "Balancing Target Flexibility and Target Denaturation in Computational Fragment-Based Inhibitor Discovery," Journal of Computational Chemistry, 33:1880-91, 2012.


68. Stavitskaya, L., Shim, J., Healy, J.R., Matsumoto, R.R., MacKerell Jr., A.D., Coop, A. "Deconstructing 14-phenylpropyloxymetopon: minimal requirements for binding to mu opioid receptors," Bioorganic & Medicinal Chemistry, 20: 4556– 4563, 2012.


69. Yu, W., He, X., Vanommeslaeghe, K. and MacKerell, A.D., Jr., "Extension of the CHARMM General Force Field to Sulfonyl-Containing Compounds and Its Utility in Biomolecular Simulations," Journal of Computational Chemistry, 33: 2451-2468, 2012, doi: 10.1002/jcc.23067, PMC3477297.


70. Best, R.B., Zhu, X., Shim, J., Lopes, P.E.M., Mittal, J., Feig, M., and MacKerell Jr., A.D. "Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 dihedral angles," Journal of Chemical Theory and Computation, 8: 3257-3273, 2012, DOI: 10.1021/ct300400x, PMC3549273.


71. Petty, A., Myshkin, E., Qin, H., Guo, H., Miao, H., Tochtrop, G.P., Hsieh, J.-T., Page, P., Liu, L., Lindner, D.J., Acharya, C., MacKerell, A.D., Jr. Ficker, E., Song, J., and Wang, B. "A Small Molecule Agonist of EphA2 Receptor Tyrosine Kinase Inhibits Tumor Cell Migration in vitro and Prostate Cancer Metastasis in vivo," PLoS One, 7: e42120., 2012, PMC3419725.


72. Wagh, B., Paul, T., Glassford, I., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B.,"Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin," ACS Medicinal Chemistry Letters, 3:1013–1018, 2012, PMC3763958, DOI: 10.1021/ml200254h.


73. McKnight, Laura; Raman, E.; Bezawada, Padmavani; Kudrimoti, Sucheta; Wilder, Paul; Hartman, Kira; Toth, Eric; Coop, Andrew; MacKerell, Alexander; Weber, David "Structure-Based Discovery of a Novel Pentamidine-Related Inibitor of the Calcium-Binding Protein S100B," ACS Medicinal Chemistry Letters, 3: 975–979, 2012, DOI: 10.1021/ml300166s, PMC3524579.


74. Vanommeslaeghe, K., and MacKerell Jr., A.D., "Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing," Journal of Chemical Information and Modeling, 52: 3144–3154, 2012, DOI: 10.1021/ci30036c, PMC3528824.


75. Vanommeslaeghe, K., Raman, E.P., and MacKerell Jr., A.D., "Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges," Journal of Chemical Information and Modeling, 52: 3155–3168, 2012, DOI: 10.1021/ci3003649, PMC3528813.


76. Xue, F., MacKerell, A.D., Jr., Heinzl, G., Mbatia, H., and Hom, K. "Room Temperature Catalyst-Free Knoevenagel Condensation: Facile Access to Isatinylidenerhodanines," Tetrahedron Letters, 54, 1700-1703, 2013.


77. Nagagarajan, S., Xue, F., and MacKerell, A.D., Jr. "Impact of substrate protonation and tautomerization states on interactions with the active site of Arginase I," Journal of Chemical Information and Modeling, 53: 452–460, 2013, PMC3590304.


78. Hom, K., Heinzl, G.A., Eakanunkul, S., Lopes, P.E.M., Xue, F., MacKerell, A.D., Jr., and Angela Wilks, A., "Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa," Journal of Medicinal Chemistry, 56: 2097-2109, 2013, PMC3643010.


79. Jung, K.-Y., Samadani, R., Chauhan, J., Nevels, K., Yap, J.L., Zhang, J., Worlikar, S., Ensey, M., Shukla, S, Salmo, R., Heinzl, G., Gordon, C., Dukes, T., Lanning, M.E., MacKerell, A.D., Jr., Shapiro, P., and Fletcher, S. "Structural Modifications of (Z)-3-(2-aminoethyl)-5-(4-ethoxybenzylidene)thiazolidine-2,4-dione that Improve Selectivity for Inhibiting Melanoma Cells Containing Active ERK Signaling," Organic & Biomolecular Chemistry, 11: 3706-3732, 2013, PMC3663054.


80. Cao, X., Yap, J.L., Newell-Rogers, M.K., Peddaboina, C., Hua, J., Papaconstantinou, H.T., Jupitor, D., Rai, A., Jung, K.-Y., Tubin, R.P., Yu, W., Vanommeslaeghe, K., Wilder, P.T., MacKerell, A.D., Jr., Fletcher, S., and Smythe, W.R., "The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein–protein interactions with Bak," Molecular Cancer, 12:42, 2013, PMC3663763.


81. Lakkaraju, K.S. Xue, F., Faden, A., and MacKerell, A.D., Jr., "Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations," Journal of Chemical Information and Modeling, 53: 1337–1349, 2013, PMC3693859.


82. Small, M., Andrade, R., and MacKerell, A.D., Jr., "Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach," PLoS Computational Biology, 9: e1003113, 2013, PMC3681621, doi:10.1371/journal.pcbi.1003113.


83. Yu, B., Liu, W., Yu, W.-M., Loh, M., Alter, S., Guvench, O., MacKerell, A.D., Jr., Tang, L.-D., and Qu, C.-K., "Targeting Protein Tyrosine Phosphatase SHP2 for the Treatment of PTPN11-Associated Malignancies," Molecular Cancer Therapeutics, 12:1738-1748. doi: 10.1158/1535-7163, PMC3769526.


84. Sandineni, A., Lin, B., MacKerell, A.D., Jr. and Cho, B.P., "Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis," Chemical Research in Toxicology, 26: 937-951, 2013, PMC3733349.


85. Healy, J., Bezawada, P., Shim, J., MacKerell, A.D., Jr., Coop, A., and Matsumoto, R. "Synthesis, Modeling and Pharmacological Evaluation of UMB 425, a Mixed μ Agonist/δ Antagonist Opioid Analgesic with Reduced Tolerance Liabilities," ACS Chemical Neuroscience, 4:1256-1266, 2013 PMC3778426.


86. Jung, K.-Y., Vanommeslaeghe, K., Lanning, M., Yap, J., Gordon, C., Wilder, P., MacKerell, A.D., Jr., and Fletcher, S., "Amphipathic α-Helix Mimetics Based on a 1,2-Diphenylacetylene Scaffold," Organics Letters, 15: 3234–3237, 2013.


87. Shim, J., Coop, A., and MacKerell, A.D., Jr."Molecular Details of the Activation of the μ-Opioid Receptor," Journal of Physical Chemistry B, 117; 7907–7917, 2013, PMC3735350.


88. Vanommeslaeghe, K., Guvench, O., and MacKerell, A.D., Jr., "Molecular Mechanics" in "Advances in Computational Structure Based Drug Discovery," special issue of Current Pharmaceutical Design, In Press, 2013.


89. Raman, E.P., and MacKerell, A.D., Jr., "Rapid estimation of hydration thermodynamics of macromolecular regions," Journal of Chemical Physics, 139: 055105, 2013, PMC3751957


90. Hatzi, K.; Jiang, Y.; Huang, C.; Garrett-Bakelman, F.; Gearhart, M. D.; Giannopoulou, E. G.; Zumbo, P.; Kirouac, K.; Bhaskara, S.; Polo, J. M., Kormaksson, M., MacKerell, A.D., Jr., Xue, F., Mason, C.E., Hiebert, S.W., Gilbert G. Prive, G.G., Cerchietti, L., Bardwell, V.J., Elemento, O., and Melnick, A. "A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters," Cell Reports, 4, 1-11, 2013, [DOI], PMC3854650


91. Wagh, B., Paul, T., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B."Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Cethromycin," ACS Medicinal Chemistry Letters, 4: 1114-1118, 2013, [DOI], PMC3901159


92. Varney, K., Bonvin, A.M.J.J., Yu, W., Ateh, E., Oashi, T., Huang, J., Diepeveen-de Buin, M., Bryant, J. Breukink, E., MacKerell, A.D., Jr., and de Leeuw, E., "Turning Defense into Offense: Development of Defensin Mimetics as Novel Antibiotics targeting Lipid II," PLoS Pathogens, 9: e1003732, 2013, [DOI], PMC3820767


93. Sabit, H., Mallajosyula, S.S., MacKerell, A.D., Jr., and Swaan P.W. "Transmembrane Domain II of the Human Bile Acid Transporter SLC10A2 Coordinates Sodium Translocation," Journal of Biological Chemistry, 288: 32349-32404, 2013, [DOI], PMC3820874


94. Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and MacKerell, A.D., Jr., "Polarizable Force Field for Peptides and Proteins based on the Classical Drude Oscillator," Journal of Chemical Theory and Computation, 2013, 9: 5430-5449 [DOI], PMC3896220


95. Raman, E.P., Yu, W., Lakkaraju, S.K., and MacKerell, A.D., Jr., "Inclusion of multiple fragment types in the Site Identification by Ligand Competitive Saturation (SILCS) approach," Journal of Chemical Information and Modeling, 53: 3384-3398, 2013, [DOI], PMC3947602


96. Oyer, J.A., Huang, X., Zheng, Y., Shim, J., Ezponda, T., Allegretta, M., Okot-Kotber, C.I., Patel, J.P., Melnick, A., Levine, R.L., Ferrando, MacKerell, A.D., Jr., Kelleher, N.L., Licht, J.D., and Popovic, R., "Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies," Leukemia, 28: 198-201, 2014. doi: 10.1038/leu.2013.204, PMC3888226


97. Sun, X., Rai, R., Deschamps, J.R., MacKerell, A.D., Jr., Faden, A.I., and Fengtian Xue, "Boc-protected 1-(3-oxocycloalkyl)ureas via a one-step Curtius rearrangement: mechanism and scope," Tetrahedron Letters, 2014, 55, 1905-1908. [DOI]


98. Yu, W., Lakkaraju, S.K., Raman, E.P., and MacKerell, A.D., Jr., "Site-Identification by Ligand Competitive Saturation (SILCS) Assisted Pharmacophore Modeling," Journal of Computer-Aided Molecular Design, 2014, 28: 491-507. [DOI], PMC4048638


99. Lakkaraju, S.K., Raman, E.P., Yu, W., and MacKerell, A.D., Jr., "Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations", Journal of Chemical Theory and Computation, 10: 2281-2290, 2014. [DOI]


100. Li, T., Yang, D., Zhong, S., Thomas, J.M., Xue, F., Liu, J., Kong, L., Voulalas, P., Hassan, H.E., Park, J.-S., MacKerell, A.D., Jr. and Smith, W., "Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson’s disease cell and mouse models," Human Molecular Genetics, 2014, 23: 6212-6222. [DOI]


101. Glassford, I., Miseon, L., Wagh, B., Velvadapu, V., Paul, T., Sandelin, G., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B.," Desmethyl Macrolides: Synthesis and Evaluation of 4-Desmethyl Telithromycin," ACS Medicinal Chemistry Letters, 2014, 5, 1021-1026. [DOI], PMC4160760


102. Vanommeslaeghe, K., and MacKerell, A.D., Jr., "CHARMM additive and polarizable force fields for biophysics and computer-aided drug design," Biochimica et Biophysica Acta: General Subjects, 2015, 1850: 861-871. [DOI], NIHMSID626201


103. Yu, W., Lakkaraju, S.K., Raman, E.P., Fang, L., and MacKerell, A.D., Jr., "Pharmacophore modeling using Site-Identification by Ligand Competitive Saturation (SILCS) with multiple probe molecules," Journal of Chemical Information and Modeling, 55: 407-420, 2015, [DOI], PMC4339487


104. Raman, E.P. and MacKerell, A.D., Jr., "Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability," Journal of the American Chemical Society, 137: 2608-2621, 2015, [DOI], PMC4342289


105. Fletcher, S.F., Yu, W., Huang, J., Kwasny, S.M., Chauhan, J., Opperman, T.J., MacKerell, A.D., Jr., deLeeuw, E.P.H. "Structure-Activity Relationships of a Small-Molecule Lipid II inhibitor," Drug Design, Development and Therapy, 9: 2383-2394, 2015, [DOI], PMC4422293


106. Lakkaraju, S.K., Yu, W., Raman, E.P., Hershfeld, A.V., Fang, L., Deshpande, D.A., and MacKerell, A.D., Jr., "Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors," Journal of Chemical Information and Modeling, 55: 700-708, 2015, [DOI], PMC4372819


107. Samadani, R., Zhang, J., Brophy, A., Oashi, T., Priyakumar, U.D., Raman, E.P., St John, F.J., Jung, K.-Y., Fletcher, S., Pozharski, E., MacKerell, A.D., Jr.,* and Shapiro, P.,* "Small Molecule Inhibitors of ERK-mediated Immediate Early Gene Expression and Proliferation of Melanoma Cells Expressing Mutated BRaf," Biochemical Journal, 467: 425-438, 2015, [DOI], PMC4643458


108. He, X., Lakkaraju, S.K., Hanscom, M., Zhao, Z., Wu, J., Stoica, B., MacKerell, A.D., Jr., Faden, A.I. and Xue, F., "Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5," Bioorganic and Medicinal Chemistry, 23: 2211-2220, 2015, [DOI],PMC4697443


109. Yang, W., Sun, X., Yu, W., Rai, R., Deschamps, J., Mitchell, L., Jiang, C., MacKerell, A.D., Jr., Xue, F., "Facile Synthesis of Spirocyclic Lactams from alpha-keto Carboxylic Acids." Organic Letters, 17: 3070-3073, 2015, [DOI]


110. Passaniti, A., Brusgard, J., Choe, M., Chumsri, S., Renoud, K., MacKerell, A.D., Jr, and Sudol, M., "RUNX2 and TAZ-dependent signaling pathways regulate soluble E-Cadherin levels and tumorsphere formation in breast cancer cells," Oncotarget, 6: 28132-28150. 2015, [DOI]


111. Drennen, B., MacKerell, A.D., Jr. and Fletcher, S. "Expedient access to alpha-helix mimetics based on an isocinchomeronic acid core," Tetrahedron Letters, 56, 6819-6822, [DOI]


112. Lanning, M.E., Yu,W., Yap, J.l., Chauhan, J., Chen, L., Whiting, E., Pidugu, L.S., Atkinson, T, Bailey, H., Li, W., Roth, B.M., Hynicka,L., Chesko, K., Toth, E.A., Shapiro, P., MacKerell, Jr, A.D., Wilder, P.T. and Fletcher, F., "Structure-Based Design of N-Substituted 1-Hydroxy-4-sulfamoyl-2-naphthoates as Selective Inhibitors of the Mcl-1 Oncoprotein," European Journal of Medicinal Chemistry," In Press, 2016, [DOI]


113. Cavalier, M.C., Ansari, M.I., Pierce, A.D., Wilder, P.T., McKnight, L.E., Raman, E.P., Neau, D.B., Bezawada, P., Alasady, M.J., Varney, K.M., Toth, E.A., MacKerell Jr., A.D., Coop, A., Weber, D.J., "Small Molecule Inhibitors of Ca2+-S100B Reveal Two Protein Conformations," Journal of Medicinal Chemistry, 59: 592-608, 2016, PMC4732916, [DOI]


114. Glassford, I., Teija, C.N., Daher, S.S., Weil, A., Small, M.C., Redhu, S.K., Colussi, D.J., Jacobson, M.A., Childers, W., Buttaro, B., Nicholson, A.W., MacKerell, A.D., Jr., Cooperman, B.S., Andrade, R.B. "Ribosome-templated azide−alkyne cycloadditions: synthesis of potent macrolide antibiotics by in situ click chemistry," Journal of the American Chemical Society, 138: 3136-3144, 2016, PMC4785600, [DOI]


115. Cavalier, M.C., Melville, Z., Aligholizadeh, E., Raman, E.P., Yu, W., Fang, L., Alasady, M., Pierce, A.D., Wilder, P.T., MacKerell, A.D., Jr. and Weber, D.J. "Novel protein-inhibitor interactions in site 3 of Ca2+-bound S100B as discovered by X-ray crystallography," Acta Crystallographica Section D, D72, 753-760, 2016, PMC4908867, [DOI]


116. Astudillo, L, da Silva, T.G., Wang, Z., Han, X., Jin, K., VanWye, J., Zhu, X., Weaver, K.L,, Oashi, T., Lopes, P.E.M., Orton, D., Neitzel, L.R., Lee, E., Landgraf, R., Robbins, D.J., MacKerell, A.D., Jr. and Capobianco, A.J. "Inhibitor of Mastermind Recruitment (IMR-1): A Small Molecule Inhibitor of the Notch Transcriptional Activation Complex," Cancer Research, 76:3593-3603, 2016, PMC4911243, [DOI]


117. Cardenas, M.G., Yu, W.,* Beguelin, W., Teater, M., Geng, H., Goldstein, R., Oswald, E., Hatzi, K., Yang, S.-N., Cohen, J., Shaknovich, R., Vannomeslaeghe, K., Cheng, H., Liang, D., Cho, H.J., Abbott, J., Cerchietti, L, Cierpicki, T., Xue, F., MacKerell, A.D., Jr., and Melnick, A.M., "Therapeutic targeting of GCB- and ABC-DLBCLs by rationally designed BCL6 inhibitors," Journal of Clinical Investigation, 126:3351-336, 2016, PMC5004937, [DOI]


118. Soteras Gutiérrez, I., Lin, F.-Y., Vanommeslaeghe, K., Lemkul, J.A., Armacost, K.A., Brooks, Cl., III, and MacKerell, A.D., Jr., "Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved treatment of ligand-protein interactions," Bioorganic & Medicinal Chemistry, 24: 4812-4825, 2016, PMC5053860, [DOI]


119. Heinzl, G., Huang, W,. Yu, W, Giardina, B., Zhou, Y, MacKerell, A.D., Jr. Wilks, A., and Xue, F., "Benzimidoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa," Journal of Medicinal Chemistry, 2016, 59:6929-6942, 2016, PMC5080841, [DOI]


120. Sarkar, A., Yu, W., Desai, U.R., MacKerell, A.D., Jr., and Mosier, P. "Estimating glycosaminoglycan-protein interaction affinity: Water dominates the specific antithrombin–heparin Interaction," Glycobiology, 26: 1041-1047, 2016, PMC5072149, [DOI]


121. Chauhan, J., Cardinale, S., Fang, L., Huang, J., Kwasny, S.M., MacKerell, A.D., Jr., Opperman, T.J., Fletcher, S., and Erik P.H. de Leeuw, E.P.H. "Towards Development of Small Molecule Lipid II inhibitors as Novel Antibiotics," PLoS ONE, 11: e0164515, 2016, PMC5077133 [DOI]


122. Jo, S., Cheng, X., Lee, J., Kim, S., Park, S.-J., Patel, D.S., Beaven, A.H., Lee, K.I., Rui, H., Roux, B., MacKerell, A.D., Jr., Klauda, J.B., Qi, Y., and Im, W. "CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation," Journal of Computational Chemistry, In Press, 2016, PMC5403596, [DOI]


123. Huang, J., Lakkaraju, S.K., Coop, A. and MacKerell, A.D., Jr. "Conformational Heterogeneity of Intracellular Loop 3 of the μ-Opioid G-Protein Coupled Receptor," Journal of Physical Chemistry B, 120: 11897-11904, 2016, PMC5148698 [DOI]


124. Raman, E.P., Lakkaraju, S.K., Denny, R.A., and MacKerell, A.D., Jr. "Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by ligand competitive saturation approaches," Journal of Computational Chemistry, 38: 1238-1251, 2017, PMC5403604 [DOI]


125. Cardenas, M.G., Oswald, E., Yu, W. Xue, F., MacKerell, A.D., Jr. and Melnick, "The expanding role of the BCL6 oncoprotein as a cancer therapeutic target," Clinical Cancer Research, 23:885-893, 2017, PMC5315622, [DOI]


126. Yang, M., Simon, R., and MacKerell, A.D., Jr. "Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4: Implications for Vaccine Design," Journal of Physical Chemistry B, 121: 3412-3423, 2017, PMC5407322, [DOI]


127. Shah, N.G., Tulapurkar, M.E., Ramarathnam, A., Brophy, Martinez, R., Hom, K., Hodges, T., Samadani, R., Singh, I.S., MacKerell, A.D., Jr., Shapiro, P., and Hasday, J.D., "Novel Non-catalytic Substrate-selective p38α-specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-inflammatory Activity," The Journal of Immunology, 198: 3296-3306, 2017, PMC5649369, [DOI]


128. Liang, D., Yu, W., Nguyen, N., Deschamps, J., Imler, G., Li, Yue; MacKerell, A.D., Jr., Jiang, C., and Xue, F. "Iodobenzene-Catalyzed Synthesis of Phenanthridinones via Oxidative C-H Amidation," The Journal of Organic Chemistry, 82 82: 3589-3596, 2017, [DOI]


129. Baliban, S.M., Yang, M., Ramachandran, G., Curtis, B., Shridhar, S., Laufer, R.S., Wang, J.Y., Van Druff, J., Higginson, E.E., Hegerle, N., Varney, K.M., Galen, J.E., Tennant, S.M, Lees, A., MacKerell, A.D., Jr., Levine, M.M., and Simon, R., "A Salmonella Typhimurium glycoconjugate vaccine that targets invasive infections in sub-Saharan Africa," PLOS Neglected Tropical Diseases, 11: e0005493, 2017, PMC5397072, [DOI]


130. Yang, M., Huang, J., Simon, R., Wang, L.-X., and MacKerell, A.D., Jr., "Conformational Heterogeneity of the HIV Envelope Glycan Shield," Scientific Reports, 7: 4435, 2017, PMC5493700, [DOI]


131. Lin, F.-Y., and MacKerell, A.D., Jr., "Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding?" The Journal of Physical Chemistry B, 121: 6813-6821, 2017, PMC5523114, [DOI]


132. Klontz, E., Adam Tomich, A., Gunther, S., Lemkul, J.A., Deredge, D., Silverstein, Z., Shaw, J., McElheny, C., Doi, Y., Wintrode, P., MacKerell, A.D., Jr., Sluis-Cremer, N., and Sundberg, E., "Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumoniae and Escherichia coli," Antimicrobial Agents and Chemotherapy, 61: e01572-17, 2017, PMC5655077, [DOI]