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Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design.

Aytenfisu AH, Simon R, MacKerell AD Jr.

Carbohydr Res. 2019 Mar 1;475:39-47. doi: 10.1016/j.carres.2019.02.003. Epub 2019 Feb 18.


Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization.

Heid E, Fleck M, Chatterjee P, Schröder C, MacKerell AD Jr.

J Chem Theory Comput. 2019 Mar 12. doi: 10.1021/acs.jctc.8b01289. [Epub ahead of print]


Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2+".

Villa F, MacKerell AD Jr, Roux B, Simonson T.

J Phys Chem A. 2019 Jan 17;123(2):629. doi: 10.1021/acs.jpca.8b12337. Epub 2019 Jan 2. No abstract available.


Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology.

Yu W, Jo S, Lakkaraju SK, Weber DJ, MacKerell AD Jr.

Proteins. 2019 Apr;87(4):289-301. doi: 10.1002/prot.25650. Epub 2019 Jan 10.


Cation-π interactions between methylated ammonium groups and tryptophan in the CHARMM36 additive force field.

Khan HM, MacKerell AD, Reuter N.

J Chem Theory Comput. 2018 Dec 18. doi: 10.1021/acs.jctc.8b00839. [Epub ahead of print]


Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.

Brocke SA, Degen A, MacKerell AD Jr, Dutagaci B, Feig M.

J Chem Inf Model. 2019 Mar 25;59(3):1147-1162. doi: 10.1021/acs.jcim.8b00648. Epub 2018 Dec 27.


Polarizable force field for RNA based on the classical drude oscillator.

Lemkul JA, MacKerell AD Jr.

J Comput Chem. 2018 Dec 15;39(32):2624-2646. doi: 10.1002/jcc.25709.


Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields.

Lin FY, MacKerell AD Jr.

J Chem Inf Model. 2019 Jan 28;59(1):215-228. doi: 10.1021/acs.jcim.8b00616. Epub 2018 Nov 27.


A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM.

Molecules. 2018 Oct 19;23(10). pii: E2695. doi: 10.3390/molecules23102695.


Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water.

Sun D, Lakkaraju SK, Jo S, MacKerell AD Jr.

J Chem Theory Comput. 2018 Oct 9;14(10):5290-5302. doi: 10.1021/acs.jctc.8b00604. Epub 2018 Sep 14.


An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia.

Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJ, Crispino JD, MacKerell AD Jr, Bennett RL, Kelleher NL, Licht JD.

Oncogene. 2019 Jan;38(5):671-686. doi: 10.1038/s41388-018-0474-y. Epub 2018 Aug 31.


Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.

Cheng H, Linhares BM, Yu W, Cardenas MG, Ai Y, Jiang W, Winkler A, Cohen S, Melnick A, MacKerell A Jr, Cierpicki T, Xue F.

J Med Chem. 2018 Sep 13;61(17):7573-7588. doi: 10.1021/acs.jmedchem.8b00040. Epub 2018 Jul 17.


Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2.

Villa F, MacKerell AD Jr, Roux B, Simonson T.

J Phys Chem A. 2018 Jul 26;122(29):6147-6155. doi: 10.1021/acs.jpca.8b04418. Epub 2018 Jul 18. Erratum in: J Phys Chem A. 2019 Jan 17;123(2):629.


Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.

Aleksandrov A, Lin FY, Roux B, MacKerell AD Jr.

J Comput Chem. 2018 Aug 15;39(22):1707-1719. doi: 10.1002/jcc.25345. Epub 2018 May 8.


Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.

Huang J, Lemkul JA, Eastman PK, MacKerell AD Jr.

J Comput Chem. 2018 Aug 5;39(21):1682-1689. doi: 10.1002/jcc.25339. Epub 2018 May 4.


CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.

Aytenfisu AH, Yang M, MacKerell AD Jr.

J Chem Theory Comput. 2018 Jun 12;14(6):3132-3143. doi: 10.1021/acs.jctc.8b00175. Epub 2018 May 4.


Optimized Lennard-Jones Parameters for Druglike Small Molecules.

Boulanger E, Huang L, Rupakheti C, MacKerell AD Jr, Roux B.

J Chem Theory Comput. 2018 Jun 12;14(6):3121-3131. doi: 10.1021/acs.jctc.8b00172. Epub 2018 May 7.


Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Lin FY, Lopes PEM, Harder E, Roux B, MacKerell AD Jr.

J Chem Inf Model. 2018 May 29;58(5):993-1004. doi: 10.1021/acs.jcim.8b00132. Epub 2018 Apr 17.


Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.

Yang M, Aytenfisu AH, MacKerell AD Jr.

Carbohydr Res. 2018 Mar 2;457:41-50. doi: 10.1016/j.carres.2018.01.004. Epub 2018 Jan 31.


Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase.

Re S, Watabe S, Nishima W, Muneyuki E, Yamaguchi Y, MacKerell AD Jr, Sugita Y.

Sci Rep. 2018 Jan 26;8(1):1644. doi: 10.1038/s41598-018-20012-0.


Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.

Lin FY, MacKerell AD Jr.

J Chem Theory Comput. 2018 Feb 13;14(2):1083-1098. doi: 10.1021/acs.jctc.7b01086. Epub 2018 Jan 31.


Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Huang J, Simmonett AC, Pickard FC 4th, MacKerell AD Jr, Brooks BR.

J Chem Phys. 2017 Oct 28;147(16):161702. doi: 10.1063/1.4984113.


The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.

Burns LA, Faver JC, Zheng Z, Marshall MS, Smith DGA, Vanommeslaeghe K, MacKerell AD Jr, Merz KM Jr, Sherrill CD.

J Chem Phys. 2017 Oct 28;147(16):161727. doi: 10.1063/1.5001028.


Force field development and simulations of intrinsically disordered proteins.

Huang J, MacKerell AD Jr.

Curr Opin Struct Biol. 2018 Feb;48:40-48. doi: 10.1016/ Epub 2017 Nov 5. Review.


Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli.

Klontz EH, Tomich AD, Günther S, Lemkul JA, Deredge D, Silverstein Z, Shaw JF, McElheny C, Doi Y, Wintrode PL, MacKerell AD Jr, Sluis-Cremer N, Sundberg EJ.

Antimicrob Agents Chemother. 2017 Oct 24;61(11). pii: e01572-17. doi: 10.1128/AAC.01572-17. Print 2017 Nov.


Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

Li H, Chowdhary J, Huang L, He X, MacKerell AD Jr, Roux B.

J Chem Theory Comput. 2017 Sep 12;13(9):4535-4552. doi: 10.1021/acs.jctc.7b00262. Epub 2017 Aug 8.


Conformational Heterogeneity of the HIV Envelope Glycan Shield.

Yang M, Huang J, Simon R, Wang LX, MacKerell AD Jr.

Sci Rep. 2017 Jun 30;7(1):4435. doi: 10.1038/s41598-017-04532-9.


Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding?

Lin FY, MacKerell AD Jr.

J Phys Chem B. 2017 Jul 20;121(28):6813-6821. doi: 10.1021/acs.jpcb.7b04198. Epub 2017 Jul 11.


Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4.

Yang M, Simon R, MacKerell AD Jr.

J Phys Chem B. 2017 Apr 20;121(15):3412-3423. doi: 10.1021/acs.jpcb.6b08955. Epub 2016 Dec 6.


Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

Lemkul JA, MacKerell AD Jr.

J Chem Theory Comput. 2017 May 9;13(5):2053-2071. doi: 10.1021/acs.jctc.7b00067. Epub 2017 Apr 19.


Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.

Lemkul JA, MacKerell AD Jr.

J Chem Theory Comput. 2017 May 9;13(5):2072-2085. doi: 10.1021/acs.jctc.7b00068. Epub 2017 Apr 19.


Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa.

Baliban SM, Yang M, Ramachandran G, Curtis B, Shridhar S, Laufer RS, Wang JY, Van Druff J, Higginson EE, Hegerle N, Varney KM, Galen JE, Tennant SM, Lees A, MacKerell AD Jr, Levine MM, Simon R.

PLoS Negl Trop Dis. 2017 Apr 7;11(4):e0005493. doi: 10.1371/journal.pntd.0005493. eCollection 2017 Apr.


Novel Noncatalytic Substrate-Selective p38α-Specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-Inflammatory Activity.

Shah NG, Tulapurkar ME, Ramarathnam A, Brophy A, Martinez R 3rd, Hom K, Hodges T, Samadani R, Singh IS, MacKerell AD Jr, Shapiro P, Hasday JD.

J Immunol. 2017 Apr 15;198(8):3296-3306. doi: 10.4049/jimmunol.1602059. Epub 2017 Mar 15.


Iodobenzene-Catalyzed Synthesis of Phenanthridinones via Oxidative C-H Amidation.

Liang D, Yu W, Nguyen N, Deschamps JR, Imler GH, Li Y, MacKerell AD Jr, Jiang C, Xue F.

J Org Chem. 2017 Apr 7;82(7):3589-3596. doi: 10.1021/acs.joc.7b00106. Epub 2017 Mar 10.


Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

Small MC, Aytenfisu AH, Lin FY, He X, MacKerell AD Jr.

J Comput Aided Mol Des. 2017 Apr;31(4):349-363. doi: 10.1007/s10822-017-0010-0. Epub 2017 Feb 11.


An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Huang J, Mei Y, König G, Simmonett AC, Pickard FC 4th, Wu Q, Wang LP, MacKerell AD Jr, Brooks BR, Shao Y.

J Chem Theory Comput. 2017 Feb 14;13(2):679-695. doi: 10.1021/acs.jctc.6b01125. Epub 2017 Jan 24.


The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target.

Cardenas MG, Oswald E, Yu W, Xue F, MacKerell AD Jr, Melnick AM.

Clin Cancer Res. 2017 Feb 15;23(4):885-893. doi: 10.1158/1078-0432.CCR-16-2071. Epub 2016 Nov 23. Review.


Computer-Aided Drug Design Methods.

Yu W, MacKerell AD Jr.

Methods Mol Biol. 2017;1520:85-106. doi: 10.1007/978-1-4939-6634-9_5.


CHARMM-GUI 10 years for biomolecular modeling and simulation.

Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD Jr, Klauda JB, Qi Y, Im W.

J Comput Chem. 2017 Jun 5;38(15):1114-1124. doi: 10.1002/jcc.24660. Epub 2016 Nov 14. Review.


CHARMM36m: an improved force field for folded and intrinsically disordered proteins.

Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD Jr.

Nat Methods. 2017 Jan;14(1):71-73. doi: 10.1038/nmeth.4067. Epub 2016 Nov 7.


Characterization of Mg2+ Distributions around RNA in Solution.

Lemkul JA, Lakkaraju SK, MacKerell AD Jr.

ACS Omega. 2016 Oct 31;1(4):680-688. Epub 2016 Oct 26.


Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor.

Huang J, Lakkaraju SK, Coop A, MacKerell AD Jr.

J Phys Chem B. 2016 Nov 23;120(46):11897-11904. Epub 2016 Nov 15.


Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics.

Chauhan J, Cardinale S, Fang L, Huang J, Kwasny SM, Pennington MR, Basi K, diTargiani R, Capacio BR, MacKerell AD Jr, Opperman TJ, Fletcher S, de Leeuw EP.

PLoS One. 2016 Oct 24;11(10):e0164515. doi: 10.1371/journal.pone.0164515. eCollection 2016.


Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

Khan HM, Grauffel C, Broer R, MacKerell AD Jr, Havenith RW, Reuter N.

J Chem Theory Comput. 2016 Nov 8;12(11):5585-5595. Epub 2016 Oct 13.


Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction.

Sarkar A, Yu W, Desai UR, MacKerell AD, Mosier PD.

Glycobiology. 2016 Oct;26(10):1041-1047. doi: 10.1093/glycob/cww073. Epub 2016 Jul 18.


Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.

Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang SN, Cohen J, Shaknovich R, Vanommeslaeghe K, Cheng H, Liang D, Cho HJ, Abbott J, Tam W, Du W, Leonard JP, Elemento O, Cerchietti L, Cierpicki T, Xue F, MacKerell AD Jr, Melnick AM.

J Clin Invest. 2016 Sep 1;126(9):3351-62. doi: 10.1172/JCI85795. Epub 2016 Aug 2.


Structural effects of modified ribonucleotides and magnesium in transfer RNAs.

Xu Y, MacKerell AD Jr, Nilsson L.

Bioorg Med Chem. 2016 Oct 15;24(20):4826-4834. doi: 10.1016/j.bmc.2016.06.037. Epub 2016 Jun 18.


Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions.

Soteras Gutiérrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL 3rd, MacKerell AD Jr.

Bioorg Med Chem. 2016 Oct 15;24(20):4812-4825. doi: 10.1016/j.bmc.2016.06.034. Epub 2016 Jun 18.

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