Alex MacKerell, Ph.D. - Publications

Affiliations: 
Pharmacy University of Maryland School of Medicine, Baltimore, MD, United States 
Area:
Computational chemistry, biophysics, nucleic acids, drug design
Website:
http://mackerell.umaryland.edu/MacKerell_Lab.html

325 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Bedrov D, Piquemal JP, Borodin O, MacKerell AD, Roux B, Schröder C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chemical Reviews. PMID 31141351 DOI: 10.1021/acs.chemrev.8b00763  1
2019 Ustach VD, Lakkaraju SKK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of the Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. Journal of Chemical Information and Modeling. PMID 31034213 DOI: 10.1021/acs.jcim.9b00210  1
2019 Aytenfisu AH, Simon R, MacKerell AD. Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design. Carbohydrate Research. 475: 39-47. PMID 30818097 DOI: 10.1016/j.carres.2019.02.003  1
2019 Heid E, Fleck M, Chatterjee P, Schröder C, MacKerell AD. Towards Prediction of Electrostatic Parameters for Force Fields that Explicitly Treat Electronic Polarization. Journal of Chemical Theory and Computation. PMID 30811193 DOI: 10.1021/acs.jctc.8b01289  1
2019 Villa F, MacKerell AD, Roux B, Simonson T. Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg". The Journal of Physical Chemistry. A. PMID 30600990 DOI: 10.1021/acs.jpca.8b12337  1
2018 Yu W, Jo S, Lakkaraju SK, Weber DJ, MacKerell AD. Exploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation (SILCS) methodology. Proteins. PMID 30582220 DOI: 10.1002/prot.25650  1
2018 Khan HM, MacKerell AD, Reuter N. Cation-π interactions between methylated ammonium groups and tryptophan in the CHARMM36 additive force field. Journal of Chemical Theory and Computation. PMID 30562013 DOI: 10.1021/acs.jctc.8b00839  1
2018 Brocke S, Degen A, MacKerell AD, Dutagaci B, Feig M. Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. Journal of Chemical Information and Modeling. PMID 30540459 DOI: 10.1021/acs.jcim.8b00648  1
2018 Lemkul JA, MacKerell AD. Polarizable force field for RNA based on the classical drude oscillator. Journal of Computational Chemistry. 39: 2624-2646. PMID 30515902 DOI: 10.1002/jcc.25709  1
2018 Lin FY, MacKerell AD. Improved Modeling of Halogenated Ligand-Protein Interactions using the Drude Polarizable and CHARMM Additive Empirical Force Fields. Journal of Chemical Information and Modeling. PMID 30418023 DOI: 10.1021/acs.jcim.8b00616  1
2018 König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules (Basel, Switzerland). 23. PMID 30347691 DOI: 10.3390/molecules23102695  1
2018 Sun D, Lakkaraju SK, Jo S, MacKerell AD. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water. Journal of Chemical Theory and Computation. PMID 30183291 DOI: 10.1021/acs.jctc.8b00604  1
2018 Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJ, Crispino JD, MacKerell AD, Bennett RL, Kelleher NL, Licht JD. An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia. Oncogene. PMID 30171259 DOI: 10.1038/s41388-018-0474-y  1
2018 Cheng H, Linhares B, Yu W, Cardenas MG, Ai Y, Jiang W, Winkler A, Cohen S, Melnick A, MacKerell AD, Cierpicki T, Xue F. Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 (BCL6) BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design. Journal of Medicinal Chemistry. PMID 29969259 DOI: 10.1021/acs.jmedchem.8b00040  1
2018 Villa F, MacKerell AD, Roux B, Simonson T. Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg. The Journal of Physical Chemistry. A. PMID 29966419 DOI: 10.1021/acs.jpca.8b04418  1
2018 Aleksandrov A, Lin FY, Roux B, MacKerell AD. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. Journal of Computational Chemistry. PMID 29737546 DOI: 10.1002/jcc.25345  1
2018 Huang J, Lemkul JA, Eastman PK, MacKerell AD. Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. Journal of Computational Chemistry. PMID 29727037 DOI: 10.1002/jcc.25339  1
2018 Aytenfisu AH, Yang M, MacKerell AD. CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses. Journal of Chemical Theory and Computation. PMID 29694037 DOI: 10.1021/acs.jctc.8b00175  1
2018 Boulanger E, Huang L, Rupakheti C, MacKerell AD, Roux B. Optimized Lennard-Jones Parameters for Drug-Like Small Molecules. Journal of Chemical Theory and Computation. PMID 29694035 DOI: 10.1021/acs.jctc.8b00172  1
2018 Lin FY, Lopes PE, Harder ED, Roux B, MacKerell AD. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. Journal of Chemical Information and Modeling. PMID 29624370 DOI: 10.1021/acs.jcim.8b00132  1
2018 Yang M, Aytenfisu AH, MacKerell AD. Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field. Carbohydrate Research. 457: 41-50. PMID 29422120 DOI: 10.1016/j.carres.2018.01.004  1
2018 Lin FY, MacKerell AD. Polarizable Empirical Force Field for Halogen-containing Compounds Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. PMID 29357257 DOI: 10.1021/acs.jctc.7b01086  1
2017 Huang J, Simmonett AC, Pickard FC, MacKerell AD, Brooks BR. Mapping the Drude polarizable force field onto a multipole and induced dipole model. The Journal of Chemical Physics. 147: 161702. PMID 29096511 DOI: 10.1063/1.4984113  1
2017 Burns LA, Faver JC, Zheng Z, Marshall MS, Smith DGA, Vanommeslaeghe K, MacKerell AD, Merz KM, Sherrill CD. The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions. The Journal of Chemical Physics. 147: 161727. PMID 29096505 DOI: 10.1063/1.5001028  1
2017 Huang J, MacKerell AD. Force field development and simulations of intrinsically disordered proteins. Current Opinion in Structural Biology. 48: 40-48. PMID 29080468 DOI: 10.1016/j.sbi.2017.10.008  1
2017 Klontz EH, Tomich AD, Günther S, Lemkul JA, Deredge D, Silverstein Z, Shaw JF, McElheny C, Doi Y, Wintrode P, MacKerell AD, Sluis-Cremer N, Sundberg EJ. Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumoniae and Escherichia coli. Antimicrobial Agents and Chemotherapy. PMID 28874374 DOI: 10.1128/AAC.01572-17  1
2017 Li H, Chowdhary J, Huang L, He X, MacKerell AD, Roux B. Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids. Journal of Chemical Theory and Computation. PMID 28731702 DOI: 10.1021/acs.jctc.7b00262  1
2017 Yang M, Huang J, Simon R, Wang LX, MacKerell AD. Conformational Heterogeneity of the HIV Envelope Glycan Shield. Scientific Reports. 7: 4435. PMID 28667249 DOI: 10.1038/s41598-017-04532-9  1
2017 Lin FY, MacKerell AD. Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding? The Journal of Physical Chemistry. B. PMID 28657759 DOI: 10.1021/acs.jpcb.7b04198  1
2017 Yang M, Simon R, MacKerell AD. Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4. The Journal of Physical Chemistry. B. 121: 3412-3423. PMID 28423910 DOI: 10.1021/acs.jpcb.6b08955  1
2017 Lemkul JA, MacKerell AD. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics. Journal of Chemical Theory and Computation. 13: 2053-2071. PMID 28399366 DOI: 10.1021/acs.jctc.7b00067  1
2017 Lemkul JA, MacKerell AD. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA. Journal of Chemical Theory and Computation. PMID 28398748 DOI: 10.1021/acs.jctc.7b00068  1
2017 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, et al. Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa. Plos Neglected Tropical Diseases. 11: e0005493. PMID 28388624 DOI: 10.1371/journal.pntd.0005493  1
2017 Shah NG, Tulapurkar ME, Ramarathnam A, Brophy A, Martinez R, Hom K, Hodges T, Samadani R, Singh IS, MacKerell AD, Shapiro P, Hasday JD. Novel Noncatalytic Substrate-Selective p38α-Specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-Inflammatory Activity. Journal of Immunology (Baltimore, Md. : 1950). PMID 28298524 DOI: 10.4049/jimmunol.1602059  1
2017 Liang D, Yu W, Nguyen N, Deschamps JR, Imler GH, Li Y, MacKerell A, Jiang C, Xue F. Iodobenzene-Catalyzed Synthesis of Phenanthridinones via Oxidative C-H Amidation. The Journal of Organic Chemistry. PMID 28245353 DOI: 10.1021/acs.joc.7b00106  1
2017 Small MC, Aytenfisu AH, Lin FY, He X, MacKerell AD. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. Journal of Computer-Aided Molecular Design. PMID 28190218 DOI: 10.1007/s10822-017-0010-0  1
2017 Huang J, Mei Y, Koenig G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. Journal of Chemical Theory and Computation. PMID 28081366 DOI: 10.1021/acs.jctc.6b01125  1
2017 Yu W, MacKerell AD. Computer-Aided Drug Design Methods. Methods in Molecular Biology (Clifton, N.J.). 1520: 85-106. PMID 27873247 DOI: 10.1007/978-1-4939-6634-9_5  1
2016 Cardenas MG, Oswald E, Yu W, Xue F, MacKerell AD, Melnick AM. The expanding role of the BCL6 oncoprotein as a cancer therapeutic target. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27881582 DOI: 10.1158/1078-0432.CCR-16-2071  1
2016 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, Klauda JB, Qi Y, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/jcc.24660  1
2016 Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nature Methods. PMID 27819658 DOI: 10.1038/nmeth.4067  1
2016 Lemkul JA, Lakkaraju SK, MacKerell AD. Characterization of Mg(2+) Distributions around RNA in Solution. Acs Omega. 1: 680-688. PMID 27819065 DOI: 10.1021/acsomega.6b00241  1
2016 Huang J, Lakkaraju SK, Coop A, MacKerell AD. Conformational Heterogeneity of Intracellular Loop 3 of the µ-Opioid G-Protein Coupled Receptor. The Journal of Physical Chemistry. B. PMID 27801588 DOI: 10.1021/acs.jpcb.6b09351  1
2016 Raman EP, Lakkaraju SK, Denny RA, MacKerell AD. 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. PMID 27782307 DOI: 10.1002/jcc.24522  1
2016 Chauhan J, Cardinale S, Fang L, Huang J, Kwasny SM, Pennington MR, Basi K, diTargiani R, Capacio BR, MacKerell AD, Opperman TJ, Fletcher S, de Leeuw EP. Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics. Plos One. 11: e0164515. PMID 27776124 DOI: 10.1371/journal.pone.0164515  1
2016 Lemkul JA, MacKerell AD. Balancing the Interactions of Mg(2+) in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model. The Journal of Physical Chemistry. B. 120: 11436-11448. PMID 27759379 DOI: 10.1021/acs.jpcb.6b09262  1
2016 Khan HM, Grauffel C, Broer R, MacKerell AD, Havenith RW, Reuter N. Improving the force field description of tyrosine-choline cation-π interactions: QM investigation of phenol-N(Me)4+ interactions. Journal of Chemical Theory and Computation. PMID 27682345 DOI: 10.1021/acs.jctc.6b00654  1
2016 Sarkar A, Yu W, Desai UR, MacKerell AD, Mosier PD. Estimating glycosaminoglycan-protein interaction affinity: Water dominates the specific antithrombin-heparin interaction. Glycobiology. PMID 27496757 DOI: 10.1093/glycob/cww073  1
2016 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, ... ... MacKerell AD, et al. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. The Journal of Clinical Investigation. PMID 27482887 DOI: 10.1172/JCI85795  1
2016 Xu Y, MacKerell AD, Nilsson L. Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorganic & Medicinal Chemistry. PMID 27364608 DOI: 10.1016/j.bmc.2016.06.037  1
2016 Soteras Gutiérrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL, MacKerell AD. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. Bioorganic & Medicinal Chemistry. PMID 27353885 DOI: 10.1016/j.bmc.2016.06.034  1
2016 Heinzl GA, Huang W, Yu W, Giardina BJ, Zhou Y, MacKerell AD, Wilks A, Xue F. Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa. Journal of Medicinal Chemistry. PMID 27353344 DOI: 10.1021/acs.jmedchem.6b00757  1
2016 Yang M, Angles d'Ortoli T, Säwén E, Jana M, Widmalm G, MacKerell AD. Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations. Physical Chemistry Chemical Physics : Pccp. PMID 27346493 DOI: 10.1039/c6cp02970a  1
2016 Cavalier MC, Melville Z, Aligholizadeh E, Raman EP, Yu W, Fang L, Alasady M, Pierce AD, Wilder PT, MacKerell AD, Weber DJ. Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography. Acta Crystallographica. Section D, Structural Biology. 72: 753-760. PMID 27303795 DOI: 10.1107/S2059798316005532  1
2016 Feng Y, Huang J, Kim S, Shim JH, MacKerell AD, Ge NH. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation. The Journal of Physical Chemistry. B. PMID 27299801 DOI: 10.1021/acs.jpcb.6b02608  1
2016 Astudillo L, da Silva TG, Wang Z, Han X, Jin K, VanWye J, Zhu X, Weaver KL, Oashi T, Lopes PE, Orton D, Neitzel LR, Lee E, Landgraf R, Robbins DJ, ... MacKerell AD, et al. The small molecule IMR-1 inhibits the Notch transcriptional activation complex to suppress tumorigenesis. Cancer Research. PMID 27197169 DOI: 10.1158/0008-5472.CAN-16-0061  1
2016 Lanning ME, Yu W, Yap JL, Chauhan J, Chen L, Whiting E, Pidugu LS, Atkinson T, Bailey H, Li W, Roth BM, Hynicka L, Chesko K, Toth EA, Shapiro P, ... MacKerell AD, et al. 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. 113: 273-292. PMID 26985630 DOI: 10.1016/j.ejmech.2016.02.006  1
2016 Glassford I, Teijaro CN, Daher SS, Weil A, Small MC, Redhu SK, Colussi DJ, Jacobson MA, Childers WE, Buttaro B, Nicholson AW, MacKerell AD, Cooperman BS, Andrade RB. Ribosome-templated azide-alkyne cycloadditions: synthesis of potent macrolide antibiotics by in situ click chemistry. Journal of the American Chemical Society. PMID 26878192 DOI: 10.1021/jacs.5b13008  1
2016 Xu Y, Vanommeslaeghe K, Aleksandrov A, MacKerell AD, Nilsson L. Additive CHARMM force field for naturally occurring modified ribonucleotides. Journal of Computational Chemistry. PMID 26841080 DOI: 10.1002/jcc.24307  1
2016 Lemkul JA, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chemical Reviews. PMID 26815602 DOI: 10.1021/acs.chemrev.5b00505  1
2016 Cavalier MC, Ansari MI, Pierce AD, Wilder PT, McKnight LE, Raman EP, Neau DB, Bezawada P, Alasady MJ, Charpentier TH, Varney K, Toth EA, MacKerell AD, Coop A, Weber DJ. Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. Journal of Medicinal Chemistry. PMID 26727270 DOI: 10.1021/acs.jmedchem.5b01369  1
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/acs.jctc.5b00935  1
2015 Lemkul JA, Huang J, MacKerell AD. Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides. The Journal of Physical Chemistry. B. PMID 26629591 DOI: 10.1021/acs.jpcb.5b09978  1
2015 Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophysical Journal. 109: 2090-2100. PMID 26588568 DOI: 10.1016/j.bpj.2015.10.009  1
2015 Savelyev A, MacKerell AD. Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding. Journal of Chemical Theory and Computation. 11: 4473-85. PMID 26575937 DOI: 10.1021/acs.jctc.5b00508  1
2015 Domene C, Jorgensen C, Vanommeslaeghe K, Schofield CJ, MacKerell A. Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor. Journal of Chemical Theory and Computation. 11: 3946-54. PMID 26574473 DOI: 10.1021/acs.jctc.5b00411  1
2015 Lakkaraju SK, Lemkul JA, Huang J, MacKerell AD. DIRECT-ID: An automated method to identify and quantify conformational variations-application to β2 -adrenergic GPCR. Journal of Computational Chemistry. PMID 26558323 DOI: 10.1002/jcc.24231  1
2015 Brusgard JL, Choe M, Chumsri S, Renoud K, MacKerell AD, Sudol M, Passaniti A. RUNX2 and TAZ-dependent signaling pathways regulate soluble E-Cadherin levels and tumorsphere formation in breast cancer cells. Oncotarget. 6: 28132-50. PMID 26320173 DOI: 10.18632/oncotarget.4654  1
2015 Mei Y, Wang Y, Kumari P, Shetty AC, Clark D, Gable T, MacKerell AD, Ma MZ, Weber DJ, Yang AJ, Edelman MJ, Mao L. A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells. Nature Communications. 6: 7316. PMID 26095918 DOI: 10.1038/ncomms8316  1
2015 Yang M, Huang J, MacKerell AD. Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension. Journal of Chemical Theory and Computation. 11: 2855-2867. PMID 26082676 DOI: 10.1021/acs.jctc.5b00243  1
2015 Yang W, Sun X, Yu W, Rai R, Deschamps JR, Mitchell LA, Jiang C, MacKerell AD, Xue F. Facile Synthesis of Spirocyclic Lactams from β-Keto Carboxylic Acids. Organic Letters. 17: 3070-3. PMID 26043081 DOI: 10.1021/acs.orglett.5b01350  1
2015 Chen W, Shi C, MacKerell AD, Shen J. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields. The Journal of Physical Chemistry. B. 119: 7902-10. PMID 26020564 DOI: 10.1021/acs.jpcb.5b02290  1
2015 Jana M, MacKerell AD. CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides. The Journal of Physical Chemistry. B. 119: 7846-59. PMID 26018564 DOI: 10.1021/acs.jpcb.5b01767  1
2015 Fletcher S, Yu W, Huang J, Kwasny SM, Chauhan J, Opperman TJ, MacKerell AD, de Leeuw E. Structure-activity exploration of a small-molecule Lipid II inhibitor. Drug Design, Development and Therapy. 9: 2383-94. PMID 25987836 DOI: 10.2147/DDDT.S79504  1
2015 Lemkul JA, Roux B, van der Spoel D, MacKerell AD. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. Journal of Computational Chemistry. 36: 1473-9. PMID 25962472 DOI: 10.1002/jcc.23937  1
2015 Lakkaraju SK, Mbatia H, Hanscom M, Zhao Z, Wu J, Stoica B, MacKerell AD, Faden AI, Xue F. Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5. Bioorganic & Medicinal Chemistry Letters. 25: 2275-9. PMID 25937015 DOI: 10.1016/j.bmcl.2015.04.042  1
2015 Mistry P, Laird MH, Schwarz RS, Greene S, Dyson T, Snyder GA, Xiao TS, Chauhan J, Fletcher S, Toshchakov VY, MacKerell AD, Vogel SN. Inhibition of TLR2 signaling by small molecule inhibitors targeting a pocket within the TLR2 TIR domain. Proceedings of the National Academy of Sciences of the United States of America. 112: 5455-60. PMID 25870276 DOI: 10.1073/pnas.1422576112  1
2015 Vanommeslaeghe K, Yang M, MacKerell AD. Robustness in the fitting of molecular mechanics parameters. Journal of Computational Chemistry. 36: 1083-101. PMID 25826578 DOI: 10.1002/jcc.23897  1
2015 He X, Lakkaraju SK, Hanscom M, Zhao Z, Wu J, Stoica B, MacKerell AD, Faden AI, Xue F. Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5. Bioorganic & Medicinal Chemistry. 23: 2211-20. PMID 25801156 DOI: 10.1016/j.bmc.2015.02.054  1
2015 Mallajosyula SS, Jo S, Im W, MacKerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods in Molecular Biology (Clifton, N.J.). 1273: 407-29. PMID 25753723 DOI: 10.1007/978-1-4939-2343-4_25  1
2015 Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods in Molecular Biology (Clifton, N.J.). 1273: 391-406. PMID 25753722 DOI: 10.1007/978-1-4939-2343-4_24  1
2015 Savelyev A, MacKerell AD. Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields. The Journal of Physical Chemistry. B. 119: 4428-40. PMID 25751286 DOI: 10.1021/acs.jpcb.5b00683  1
2015 Faller CE, Raman EP, MacKerell AD, Guvench O. Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design. Methods in Molecular Biology (Clifton, N.J.). 1289: 75-87. PMID 25709034 DOI: 10.1007/978-1-4939-2486-8_7  1
2015 Yang M, MacKerell AD. Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM). Journal of Chemical Theory and Computation. 11: 788-799. PMID 25705140 DOI: 10.1021/ct500993h  1
2015 Samadani R, Zhang J, Brophy A, Oashi T, Priyakumar UD, Raman EP, St John FJ, Jung KY, Fletcher S, Pozharski E, MacKerell AD, Shapiro P. Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf. The Biochemical Journal. 467: 425-38. PMID 25695333 DOI: 10.1042/BJ20131571  1
2015 Lakkaraju SK, Yu W, Raman EP, Hershfeld AV, Fang L, Deshpande DA, MacKerell AD. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. Journal of Chemical Information and Modeling. 55: 700-8. PMID 25692383 DOI: 10.1021/ci500729k  1
2015 Kasavajhala K, Bikkina S, Patil I, MacKerell AD, Priyakumar UD. Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution. The Journal of Physical Chemistry. B. 119: 3755-61. PMID 25668757 DOI: 10.1021/jp512414f  1
2015 Raman EP, MacKerell AD. Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability. Journal of the American Chemical Society. 137: 2608-21. PMID 25625202 DOI: 10.1021/ja512054f  1
2015 Yu W, Lakkaraju SK, Raman EP, Fang L, MacKerell AD. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. Journal of Chemical Information and Modeling. 55: 407-20. PMID 25622696 DOI: 10.1021/ci500691p  1
2015 Savelyev A, MacKerell AD. Differential Impact of the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) on DNA Conformational Properties. The Journal of Physical Chemistry Letters. 6: 212-216. PMID 25580188 DOI: 10.1021/jz5024543  1
2015 Lopes PE, Guvench O, MacKerell AD. Current status of protein force fields for molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 1215: 47-71. PMID 25330958 DOI: 10.1007/978-1-4939-1465-4_3  1
2015 Vanommeslaeghe K, MacKerell AD. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochimica Et Biophysica Acta. 1850: 861-871. PMID 25149274 DOI: 10.1016/j.bbagen.2014.08.004  1
2015 Patel DS, He X, MacKerell AD. Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator. The Journal of Physical Chemistry. B. 119: 637-52. PMID 24564643 DOI: 10.1021/jp412696m  1
2015 Domene C, Jorgensen C, Vanommeslaeghe K, Schofield CJ, MacKerell A. Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor Journal of Chemical Theory and Computation. 11: 3946-3954. DOI: 10.1021/acs.jctc.5b00411  1
2015 Drennen B, MacKerell AD, Fletcher S. Expedient access to pre-organized α-helix mimetics based on an isocinchomeronic acid core Tetrahedron Letters. 56: 6819-6822. DOI: 10.1016/j.tetlet.2015.10.020  1
2014 Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Roux B, Im W. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology. 96: 235-65. PMID 25443960 DOI: 10.1016/bs.apcsb.2014.06.002  1
2014 Kern NR, Lee HS, Wu EL, Park S, Vanommeslaeghe K, MacKerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophysical Journal. 107: 1885-95. PMID 25418169 DOI: 10.1016/j.bpj.2014.09.007  1
2014 Huang J, Lopes PE, Roux B, MacKerell AD. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. The Journal of Physical Chemistry Letters. 5: 3144-3150. PMID 25247054 DOI: 10.1021/jz501315h  1
2014 Glassford I, Lee M, Wagh B, Velvadapu V, Paul T, Sandelin G, DeBrosse C, Klepacki D, Small MC, MacKerell AD, Andrade RB. Desmethyl macrolides: synthesis and evaluation of 4-desmethyl telithromycin. Acs Medicinal Chemistry Letters. 5: 1021-6. PMID 25221660 DOI: 10.1021/ml5002097  1
2014 Huang J, MacKerell AD. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. Biophysical Journal. 107: 991-7. PMID 25140435 DOI: 10.1016/j.bpj.2014.06.038  1
2014 Mallajosyula SS, Vanommeslaeghe K, MacKerell AD. Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein. The Journal of Physical Chemistry. B. 118: 11696-706. PMID 25137353 DOI: 10.1021/jp508128d  1
2014 Li T, Yang D, Zhong S, Thomas JM, Xue F, Liu J, Kong L, Voulalas P, Hassan HE, Park JS, MacKerell AD, Smith WW. Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models. Human Molecular Genetics. 23: 6212-22. PMID 24993787 DOI: 10.1093/hmg/ddu341  1
2014 Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107: 134-45. PMID 24988348 DOI: 10.1016/j.bpj.2014.05.034  1
2014 Lemkul JA, Savelyev A, MacKerell AD. Induced Polarization Influences the Fundamental Forces in DNA Base Flipping. The Journal of Physical Chemistry Letters. 5: 2077-2083. PMID 24976900 DOI: 10.1021/jz5009517  1
2014 Lakkaraju SK, Raman EP, Yu W, MacKerell AD. 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. PMID 24932136 DOI: 10.1021/ct500201y  1
2014 Savelyev A, MacKerell AD. Balancing the interactions of ions, water, and DNA in the Drude polarizable force field. The Journal of Physical Chemistry. B. 118: 6742-57. PMID 24874104 DOI: 10.1021/jp503469s  1
2014 Kumar P, Bojarowski SA, Jarzembska KN, Domaga?a S, Vanommeslaeghe K, Mackerell AD, Dominiak PM. A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers. Journal of Chemical Theory and Computation. 10: 1652-1664. PMID 24803869 DOI: 10.1021/ct4011129  1
2014 Savelyev A, MacKerell AD. All-atom polarizable force field for DNA based on the classical Drude oscillator model. Journal of Computational Chemistry. 35: 1219-39. PMID 24752978 DOI: 10.1002/jcc.23611  1
2014 Yu W, Lakkaraju SK, Raman EP, MacKerell AD. Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. Journal of Computer-Aided Molecular Design. 28: 491-507. PMID 24610239 DOI: 10.1007/s10822-014-9728-0  1
2014 Sun X, Rai R, Deschamps JR, Mackerell AD, Faden AI, Xue F. Boc-protected 1-(3-oxocycloalkyl)ureas via a one-step Curtius rearrangement: mechanism and scope. Tetrahedron Letters. 55: 842-844. PMID 24563555 DOI: 10.1016/j.tetlet.2013.12.021  1
2014 Patel DS, Pendrill R, Mallajosyula SS, Widmalm G, MacKerell AD. Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments. The Journal of Physical Chemistry. B. 118: 2851-71. PMID 24552401 DOI: 10.1021/jp412051v  1
2014 Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Current Pharmaceutical Design. 20: 3281-92. PMID 23947650 DOI: 10.2174/13816128113199990600  1
2014 Oyer JA, Huang X, Zheng Y, Shim J, Ezponda T, Carpenter Z, Allegretta M, Okot-Kotber CI, Patel JP, Melnick A, Levine RL, Ferrando A, Mackerell AD, Kelleher NL, Licht JD, et al. Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies. Leukemia. 28: 198-201. PMID 23823660 DOI: 10.1038/leu.2013.204  1
2014 Sun X, Rai R, Mackerell AD, Faden AI, Xue F. Facile one-step synthesis of 2,5-diketopiperazines Tetrahedron Letters. 55: 1905-1908. DOI: 10.1016/j.tetlet.2014.01.133  1
2013 Wagh B, Paul T, Debrosse C, Klepacki D, Small MC, Mackerell AD, Andrade RB. Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Cethromycin. Acs Medicinal Chemistry Letters. 4: 1114-1118. PMID 24470840 DOI: 10.1021/ml400337t  1
2013 Lopes PE, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 9: 5430-5449. PMID 24459460 DOI: 10.1021/ct400781b  1
2013 Raman EP, Yu W, Lakkaraju SK, MacKerell AD. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. Journal of Chemical Information and Modeling. 53: 3384-98. PMID 24245913 DOI: 10.1021/ci4005628  1
2013 Varney KM, Bonvin AM, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, Diepeveen-de Buin M, Bryant J, Breukink E, Mackerell AD, de Leeuw EP. Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. Plos Pathogens. 9: e1003732. PMID 24244161 DOI: 10.1371/journal.ppat.1003732  1
2013 Sabit H, Mallajosyula SS, MacKerell AD, Swaan PW. Transmembrane domain II of the human bile acid transporter SLC10A2 coordinates sodium translocation. The Journal of Biological Chemistry. 288: 32394-404. PMID 24045943 DOI: 10.1074/jbc.M113.518555  1
2013 Denning EJ, Thirumalai D, MacKerell AD. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophysical Chemistry. 184: 8-16. PMID 24012912 DOI: 10.1016/j.bpc.2013.08.002  1
2013 Lin B, Lopes PE, Roux B, MacKerell AD. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. The Journal of Chemical Physics. 139: 084509. PMID 24007020 DOI: 10.1063/1.4818731  1
2013 Lin B, He X, MacKerell AD. A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields. The Journal of Physical Chemistry. B. 117: 10572-80. PMID 23947568 DOI: 10.1021/jp4061889  1
2013 Raman EP, MacKerell AD. Rapid estimation of hydration thermodynamics of macromolecular regions. The Journal of Chemical Physics. 139: 055105. PMID 23927290 DOI: 10.1063/1.4817344  1
2013 Hatzi K, Jiang Y, Huang C, Garrett-Bakelman F, Gearhart MD, Giannopoulou EG, Zumbo P, Kirouac K, Bhaskara S, Polo JM, Kormaksson M, MacKerell AD, Xue F, Mason CE, Hiebert SW, et al. A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Reports. 4: 578-88. PMID 23911289 DOI: 10.1016/j.celrep.2013.06.016  1
2013 Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD, Roux B. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. The Journal of Physical Chemistry. B. 117: 9142-60. PMID 23841725 DOI: 10.1021/jp402860e  1
2013 Jain V, Hilton B, Lin B, Jain A, MacKerell AD, Zou Y, Cho BP. Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence. Chemical Research in Toxicology. 26: 1251-62. PMID 23841451 DOI: 10.1021/tx400186v  1
2013 Huang J, MacKerell AD. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. Journal of Computational Chemistry. 34: 2135-45. PMID 23832629 DOI: 10.1002/jcc.23354  1
2013 Yu B, Liu W, Yu WM, Loh ML, Alter S, Guvench O, Mackerell AD, Tang LD, Qu CK. Targeting protein tyrosine phosphatase SHP2 for the treatment of PTPN11-associated malignancies. Molecular Cancer Therapeutics. 12: 1738-48. PMID 23825065 DOI: 10.1158/1535-7163.MCT-13-0049-T  1
2013 Luo Y, Jiang W, Yu H, MacKerell AD, Roux B. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discussions. 160: 135-49; discussion 2. PMID 23795497 DOI: 10.1039/c2fd20068f  1
2013 Small MC, Lopes P, Andrade RB, Mackerell AD. 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. PMID 23785274 DOI: 10.1371/journal.pcbi.1003113  1
2013 Jung KY, Vanommeslaeghe K, Lanning ME, Yap JL, Gordon C, Wilder PT, MacKerell AD, Fletcher S. Amphipathic α-helix mimetics based on a 1,2-diphenylacetylene scaffold. Organic Letters. 15: 3234-7. PMID 23763721 DOI: 10.1021/ol401197n  1
2013 Shim J, Coop A, MacKerell AD. Molecular details of the activation of the μ opioid receptor. The Journal of Physical Chemistry. B. 117: 7907-17. PMID 23758404 DOI: 10.1021/jp404238n  1
2013 He X, Hatcher E, Eriksson L, Widmalm G, MacKerell AD. Bifurcated hydrogen bonding and asymmetric fluctuations in a carbohydrate crystal studied via X-ray crystallography and computational analysis. The Journal of Physical Chemistry. B. 117: 7546-53. PMID 23738792 DOI: 10.1021/jp403719g  1
2013 Healy JR, Bezawada P, Shim J, Jones JW, Kane MA, MacKerell AD, Coop A, Matsumoto RR. Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities. Acs Chemical Neuroscience. 4: 1256-66. PMID 23713721 DOI: 10.1021/cn4000428  1
2013 He X, Lopes PE, Mackerell AD. Polarizable empirical force field for acyclic polyalcohols based on the classical drude oscillator. Biopolymers. 99: 724-38. PMID 23703219 DOI: 10.1002/bip.22286  1
2013 Sandineni A, Lin B, MacKerell AD, Cho BP. Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis. Chemical Research in Toxicology. 26: 937-51. PMID 23688347 DOI: 10.1021/tx400116n  1
2013 Lakkaraju SK, Xue F, Faden AI, MacKerell AD. Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations. Journal of Chemical Information and Modeling. 53: 1337-49. PMID 23688150 DOI: 10.1021/ci400160x  1
2013 Cao X, Yap JL, Newell-Rogers MK, Peddaboina C, Jiang W, Papaconstantinou HT, Jupitor D, Rai A, Jung KY, Tubin RP, Yu W, Vanommeslaeghe K, Wilder PT, MacKerell AD, Fletcher S, et al. 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. PMID 23680104 DOI: 10.1186/1476-4598-12-42  1
2013 Mallajosyula SS, Adams KM, Barchi JJ, MacKerell AD. Conformational determinants of the activity of antiproliferative factor glycopeptide. Journal of Chemical Information and Modeling. 53: 1127-37. PMID 23627670 DOI: 10.1021/ci400147s  1
2013 Jung KY, Samadani R, Chauhan J, Nevels K, Yap JL, Zhang J, Worlikar S, Lanning ME, Chen L, Ensey M, Shukla S, Salmo R, Heinzl G, Gordon C, Dukes T, ... MacKerell AD, et al. Structural modifications of (Z)-3-(2-aminoethyl)-5-(4-ethoxybenzylidene)thiazolidine-2,4-dione that improve selectivity for inhibiting the proliferation of melanoma cells containing active ERK signaling. Organic & Biomolecular Chemistry. 11: 3706-32. PMID 23624850 DOI: 10.1039/c3ob40199e  1
2013 Hom K, Heinzl GA, Eakanunkul S, Lopes PE, Xue F, MacKerell AD, Wilks A. Small molecule antivirulents targeting the iron-regulated heme oxygenase (HemO) of P. aeruginosa. Journal of Medicinal Chemistry. 56: 2097-109. PMID 23379514 DOI: 10.1021/jm301819k  1
2013 McDonald AR, Denning EJ, MacKerell AD. Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA. The Journal of Physical Chemistry. A. 117: 1560-8. PMID 23343365 DOI: 10.1021/jp308364d  1
2013 Yu W, Lopes PE, Roux B, MacKerell AD. Six-site polarizable model of water based on the classical Drude oscillator. The Journal of Chemical Physics. 138: 034508. PMID 23343286 DOI: 10.1063/1.4774577  1
2013 Nagagarajan S, Xue F, MacKerell AD. Impact of substrate protonation and tautomerization states on interactions with the active site of arginase I. Journal of Chemical Information and Modeling. 53: 452-60. PMID 23327293 DOI: 10.1021/ci300506y  1
2013 Shim J, Zhu X, Best RB, MacKerell AD. (Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters. Journal of Computational Chemistry. 34: 593-603. PMID 23197420 DOI: 10.1002/jcc.23178  1
2013 Jain V, Hilton B, Lin B, Patnaik S, Liang F, Darian E, Zou Y, Mackerell AD, Cho BP. Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor. Nucleic Acids Research. 41: 869-80. PMID 23180767 DOI: 10.1093/nar/gks1077  1
2013 Yu W, Guvench O, MacKerell AD. Computational approaches for the design of protein-protein interaction inhibitors Understanding and Exploiting Protein-Protein Interactions as Drug Targets. 91-102. DOI: 10.4155/EBO.13.141  1
2013 Xue F, MacKerell AD, Heinzl G, Hom K. Room temperature catalyst-free Knoevenagel condensation: Facile access to isatinylidenerhodanines Tetrahedron Letters. 54: 1700-1703. DOI: 10.1016/j.tetlet.2013.01.069  1
2012 Wagh B, Paul T, Glassford I, Debrosse C, Klepacki D, Small MC, Mackerell AD, Andrade RB. Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin. Acs Medicinal Chemistry Letters. 3: 1013-1018. PMID 24015325 DOI: 10.1021/ml300230h  1
2012 Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. Journal of Chemical Theory and Computation. 8: 3257-3273. PMID 23341755 DOI: 10.1021/ct300400x  1
2012 McKnight LE, Raman EP, Bezawada P, Kudrimoti S, Wilder PT, Hartman KG, Godoy-Ruiz R, Toth EA, Coop A, Mackerell AD, Weber DJ. Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B. Acs Medicinal Chemistry Letters. 3: 975-979. PMID 23264854 DOI: 10.1021/ml300166s  1
2012 Vanommeslaeghe K, MacKerell AD. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. Journal of Chemical Information and Modeling. 52: 3144-54. PMID 23146088 DOI: 10.1021/ci300363c  1
2012 Vanommeslaeghe K, Raman EP, MacKerell AD. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. Journal of Chemical Information and Modeling. 52: 3155-68. PMID 23145473 DOI: 10.1021/ci3003649  1
2012 Raman EP, Vanommeslaeghe K, Mackerell AD. Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. Journal of Chemical Theory and Computation. 8: 3513-3525. PMID 23144598 DOI: 10.1021/ct300088r  1
2012 Zhu X, Lopes PE, Mackerell AD. Recent Developments and Applications of the CHARMM force fields. Wiley Interdisciplinary Reviews. Computational Molecular Science. 2: 167-185. PMID 23066428 DOI: 10.1002/wcms.74  1
2012 Best RB, Mittal J, Feig M, MacKerell AD. Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophysical Journal. 103: 1045-51. PMID 23009854 DOI: 10.1016/j.bpj.2012.07.042  1
2012 Petty A, Myshkin E, Qin H, Guo H, Miao H, Tochtrop GP, Hsieh JT, Page P, Liu L, Lindner DJ, Acharya C, MacKerell AD, Ficker E, Song J, 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. PMID 22916121 DOI: 10.1371/journal.pone.0042120  1
2012 Yu W, He X, Vanommeslaeghe K, MacKerell AD. Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations. Journal of Computational Chemistry. 33: 2451-68. PMID 22821581 DOI: 10.1002/jcc.23067  1
2012 Zhu X, Lopes PE, Shim J, Mackerell AD. Correction to intrinsic energy landscapes of amino acid side-chains. Journal of Chemical Information and Modeling. 52: 2317-8. PMID 22809108 DOI: 10.1021/ci300301x  1
2012 Velvadapu V, Glassford I, Lee M, Paul T, Debrosse C, Klepacki D, Small MC, Mackerell AD, Andrade RB. Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin. Acs Medicinal Chemistry Letters. 3: 211-215. PMID 22708010 DOI: 10.1021/ml200254h  1
2012 Mallajosyula SS, Guvench O, Hatcher E, Mackerell AD. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. Journal of Chemical Theory and Computation. 8: 759-776. PMID 22685386 DOI: 10.1021/ct200792v  1
2012 Stavitskaya L, Shim J, Healy JR, Matsumoto RR, MacKerell AD, Coop A. Deconstructing 14-phenylpropyloxymetopon: minimal requirements for binding to mu opioid receptors. Bioorganic & Medicinal Chemistry. 20: 4556-63. PMID 22677527 DOI: 10.1016/j.bmc.2012.05.006  1
2012 Foster TJ, MacKerell AD, Guvench O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. Journal of Computational Chemistry. 33: 1880-91. PMID 22641475 DOI: 10.1002/jcc.23026  1
2012 Zhu X, Lopes PE, Shim J, MacKerell AD. Intrinsic energy landscapes of amino acid side-chains. Journal of Chemical Information and Modeling. 52: 1559-72. PMID 22582825 DOI: 10.1021/ci300079j  1
2012 Maiti A, Noon MS, MacKerell AD, Pozharski E, Drohat AC. Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Proceedings of the National Academy of Sciences of the United States of America. 109: 8091-6. PMID 22573813 DOI: 10.1073/pnas.1201010109  1
2012 Willis CD, Oashi T, Busby B, Mackerell AD, Bloch RJ. Hydrophobic residues in small ankyrin 1 participate in binding to obscurin. Molecular Membrane Biology. 29: 36-51. PMID 22416964 DOI: 10.3109/09687688.2012.660709  1
2012 Yap JL, Cao X, Vanommeslaeghe K, Jung KY, Peddaboina C, Wilder PT, Nan A, MacKerell AD, Smythe WR, Fletcher S. Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors. Organic & Biomolecular Chemistry. 10: 2928-33. PMID 22395339 DOI: 10.1039/c2ob07125h  1
2012 Hart K, Foloppe N, Baker CM, Denning EJ, Nilsson L, Mackerell AD. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. Journal of Chemical Theory and Computation. 8: 348-362. PMID 22368531 DOI: 10.1021/ct200723y  1
2012 González PM, Hussainzada N, Swaan PW, Mackerell AD, Polli JE. 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: 1821-31. PMID 22354836 DOI: 10.1007/s11095-012-0706-8  1
2012 Yu W, Wu Z, Chen H, Liu X, MacKerell AD, Lin Z. Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures. The Journal of Physical Chemistry. B. 116: 2269-83. PMID 22260814 DOI: 10.1021/jp207807a  1
2012 Denning EJ, MacKerell AD. Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. Journal of the American Chemical Society. 134: 2800-6. PMID 22242623 DOI: 10.1021/ja211328g  1
2012 Underwood KF, D'Souza DR, Mochin-Peters M, Pierce AD, Kommineni S, Choe M, Bennett J, Gnatt A, Habtemariam B, MacKerell AD, Passaniti A. Regulation of RUNX2 transcription factor-DNA interactions and cell proliferation by vitamin D3 (cholecalciferol) prohormone activity. Journal of Bone and Mineral Research : the Official Journal of the American Society For Bone and Mineral Research. 27: 913-25. PMID 22189971 DOI: 10.1002/jbmr.1504  1
2012 Kolhatkar V, Diao L, Acharya C, Mackerell AD, Polli JE. Identification of novel nonsteroidal compounds as substrates or inhibitors of hASBT. Journal of Pharmaceutical Sciences. 101: 116-26. PMID 22109685 DOI: 10.1002/jps.22728  1
2012 Baker CM, Darian E, MacKerell AD. Towards biomolecular simulations with explicit inclusion of polarizability: Development of a CHARMM polarizable force field based on the classical drude oscillator model Rsc Biomolecular Sciences. 1: 23-50.  1
2011 Guvench O, Mallajosyula SS, Raman EP, Hatcher E, Vanommeslaeghe K, Foster TJ, Jamison FW, Mackerell AD. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. Journal of Chemical Theory and Computation. 7: 3162-3180. PMID 22125473 DOI: 10.1021/ct200328p  1
2011 Fribourg M, Moreno JL, Holloway T, Provasi D, Baki L, Mahajan R, Park G, Adney SK, Hatcher C, Eltit JM, Ruta JD, Albizu L, Li Z, Umali A, Shim J, ... ... MacKerell AD, et al. Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs. Cell. 147: 1011-23. PMID 22118459 DOI: 10.1016/j.cell.2011.09.055  1
2011 Xu Z, Chen YW, Battu A, Wilder P, Weber D, Yu W, Mackerell AD, Chen LM, Chai KX, Johnson MD, Lin CY. Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade. Journal of Medicinal Chemistry. 54: 7567-78. PMID 21966950 DOI: 10.1021/jm200920s  1
2011 Barr D, Oashi T, Burkhard K, Lucius S, Samadani R, Zhang J, Shapiro P, MacKerell AD, van der Vaart A. Importance of domain closure for the autoactivation of ERK2. Biochemistry. 50: 8038-48. PMID 21842857 DOI: 10.1021/bi200503a  1
2011 Mallajosyula SS, MacKerell AD. Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides. The Journal of Physical Chemistry. B. 115: 11215-29. PMID 21823626 DOI: 10.1021/jp203695t  1
2011 Jo S, Song KC, Desaire H, MacKerell AD, Im W. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. Journal of Computational Chemistry. 32: 3135-41. PMID 21815173 DOI: 10.1002/jcc.21886  1
2011 Pastor RW, Mackerell AD. Development of the CHARMM Force Field for Lipids. The Journal of Physical Chemistry Letters. 2: 1526-1532. PMID 21760975 DOI: 10.1021/jz200167q  1
2011 Shim J, Mackerell AD. Computational ligand-based rational design: Role of conformational sampling and force fields in model development. Medchemcomm. 2: 356-370. PMID 21716805 DOI: 10.1039/C1MD00044F  1
2011 Velvadapu V, Paul T, Wagh B, Klepacki D, Guvench O, Mackerell A, Andrade RB. Desmethyl Macrolide Analogues to Address Antibiotic Resistance: Total Synthesis and Biological Evaluation of 4,8,10-Tridesmethyl Telithromycin. Acs Medicinal Chemistry Letters. 2: 68-72. PMID 21643527 DOI: 10.1021/ml1002184  1
2011 Jiang W, Hardy DJ, Phillips JC, Mackerell AD, Schulten K, Roux B. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. The Journal of Physical Chemistry Letters. 2: 87-92. PMID 21572567 DOI: 10.1021/jz101461d  1
2011 Shim J, Coop A, MacKerell AD. Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore. The Journal of Physical Chemistry. B. 115: 7487-96. PMID 21563754 DOI: 10.1021/jp202542g  1
2011 Denning EJ, Priyakumar UD, Nilsson L, Mackerell AD. Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. Journal of Computational Chemistry. 32: 1929-43. PMID 21469161 DOI: 10.1002/jcc.21777  1
2011 Raman EP, Yu W, Guvench O, Mackerell AD. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. Journal of Chemical Information and Modeling. 51: 877-96. PMID 21456594 DOI: 10.1021/ci100462t  1
2011 Denning EJ, MacKerell AD. Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations Journal of the American Chemical Society. 133: 5770-5772. PMID 21443192 DOI: 10.1021/ja201213b  1
2011 Ringer AL, Mackerell AD. Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach. The Journal of Physical Chemistry Letters. 2011: 553-556. PMID 21423871 DOI: 10.1021/jz101657s  1
2011 Darian E, Guvench O, Yu B, Qu CK, MacKerell AD. Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase. Proteins. 79: 1573-88. PMID 21365683 DOI: 10.1002/prot.22984  1
2011 Busby B, Oashi T, Willis CD, Ackermann MA, Kontrogianni-Konstantopoulos A, Mackerell AD, Bloch RJ. Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies. Journal of Molecular Biology. 408: 321-34. PMID 21333652 DOI: 10.1016/j.jmb.2011.01.053  1
2011 Boston SR, Deshmukh R, Strome S, Priyakumar UD, MacKerell AD, Shapiro P. Characterization of ERK docking domain inhibitors that induce apoptosis by targeting Rsk-1 and caspase-9. Bmc Cancer. 11: 7. PMID 21219631 DOI: 10.1186/1471-2407-11-7  1
2011 Abel S, Dupradeau FY, Raman EP, MacKerell AD, Marchi M. Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. The Journal of Physical Chemistry. B. 115: 487-99. PMID 21192681 DOI: 10.1021/jp109545v  1
2011 Baker CM, Anisimov VM, MacKerell AD. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. The Journal of Physical Chemistry. B. 115: 580-96. PMID 21166469 DOI: 10.1021/jp1092338  1
2011 Hatcher E, Säwén E, Widmalm G, MacKerell AD. Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides. The Journal of Physical Chemistry. B. 115: 597-608. PMID 21158455 DOI: 10.1021/jp109475p  1
2011 Oashi T, Ringer AL, Raman EP, Mackerell AD. Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness. Journal of Chemical Information and Modeling. 51: 148-58. PMID 21142079 DOI: 10.1021/ci100359a  1
2011 Yap JL, Worlikar S, MacKerell AD, Shapiro P, Fletcher S. Small-molecule inhibitors of the ERK signaling pathway: Towards novel anticancer therapeutics. Chemmedchem. 6: 38-48. PMID 21110380 DOI: 10.1002/cmdc.201000354  1
2011 Acharya C, Coop A, Polli JE, Mackerell AD. Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Current Computer-Aided Drug Design. 7: 10-22. PMID 20807187 DOI: 10.2174/157340911793743547  1
2011 Baker CM, Anisimov VM, MacKerell AD. Development of CHARMM polarizable force field for nucleic acid bases based on the classical drude oscillator model Journal of Physical Chemistry B. 115: 580-596. DOI: 10.1021/jp1092338  1
2010 Cunningham CW, Hom K, Acharya C, Wilks A, Mackerell AD, Coop A. Synthesis and Characterization of a Novel Diels - Alder Adduct of Codeine. Helvetica Chimica Acta. 93: 220-226. PMID 23378668 DOI: 10.1002/hlca.200900234  1
2010 Wilder PT, Charpentier TH, Liriano MA, Gianni K, Varney KM, Pozharski E, Coop A, Toth EA, Mackerell AD, Weber DJ. In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction. International Journal of High Throughput Screening. 2010: 109-126. PMID 21132089 DOI: 10.2147/IJHTS.S8210  1
2010 Rais R, Acharya C, MacKerell AD, Polli JE. Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates Molecular Pharmaceutics. 7: 2240-2254. PMID 20939504 DOI: 10.1021/mp100233v  1
2010 West AL, St John F, Lopes PE, MacKerell AD, Pozharski E, Michel SL. Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites. Journal of the American Chemical Society. 132: 14447-56. PMID 20863122 DOI: 10.1021/ja104118r  1
2010 Raman EP, Guvench O, MacKerell AD. CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. The Journal of Physical Chemistry. B. 114: 12981-94. PMID 20845956 DOI: 10.1021/jp105758h  1
2010 Venable RM, Hatcher E, Guvench O, Mackerell AD, Pastor RW. Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. The Journal of Physical Chemistry. B. 114: 12501-7. PMID 20831149 DOI: 10.1021/jp105549s  1
2010 Semenyuk A, Darian E, Liu J, Majumdar A, Cuenoud B, Miller PS, Mackerell AD, Seidman MM. Targeting of an interrupted polypurine:polypyrimidine sequence in mammalian cells by a triplex-forming oligonucleotide containing a novel base analogue. Biochemistry. 49: 7867-78. PMID 20701359 DOI: 10.1021/bi100797z  1
2010 He X, Guvench O, Mackerell AD, Klein ML. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface. The Journal of Physical Chemistry. B. 114: 9787-94. PMID 20614916 DOI: 10.1021/jp101860v  1
2010 Huang N, Kolhatkar R, Eyobo Y, Sorci L, Rodionova I, Osterman AL, MacKerell AD, Zhang H. Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: Implication for structure-based drug design and improvement Journal of Medicinal Chemistry. 53: 5229-5239. PMID 20578699 DOI: 10.1021/jm100377f  1
2010 Zhu X, Mackerell AD. Polarizable empirical force field for sulfur-containing compounds based on the classical drude oscillator model Journal of Computational Chemistry. 31: 2330-2341. PMID 20575015 DOI: 10.1002/jcc.21527  1
2010 Rais R, Acharya C, Tririya G, MacKerell AD, Polli JE. Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter Journal of Medicinal Chemistry. 53: 4749-4760. PMID 20504026 DOI: 10.1021/jm1003683  1
2010 Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. The Journal of Physical Chemistry. B. 114: 7830-43. PMID 20496934 DOI: 10.1021/jp101759q  1
2010 Baker CM, Lopes PE, Zhu X, Roux B, Mackerell AD. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 1181-1198. PMID 20401166 DOI: 10.1021/ct9005773  1
2010 Cerchietti LC, Ghetu AF, Zhu X, Da Silva GF, Zhong S, Matthews M, Bunting KL, Polo JM, Farès C, Arrowsmith CH, Yang SN, Garcia M, Coop A, Mackerell AD, Privé GG, et al. A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell. 17: 400-11. PMID 20385364 DOI: 10.1016/j.ccr.2009.12.050  1
2010 Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD, Roux B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 774-786. PMID 20300554 DOI: 10.1021/ct900576a  1
2010 Priyakumar UD, MacKerell AD. Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch Journal of Molecular Biology. 396: 1422-1438. PMID 20026131 DOI: 10.1016/j.jmb.2009.12.024  1
2010 Baker CM, MacKerell AD. Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers Journal of Molecular Modeling. 16: 567-576. PMID 19705172 DOI: 10.1007/s00894-009-0572-4  1
2010 Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry. 31: 671-90. PMID 19575467 DOI: 10.1002/jcc.21367  1
2009 Lopes PE, Roux B, Mackerell AD. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theoretical Chemistry Accounts. 124: 11-28. PMID 20577578 DOI: 10.1007/s00214-009-0617-x  1
2009 Guvench O, Hatcher ER, Venable RM, Pastor RW, Mackerell AD. CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. Journal of Chemical Theory and Computation. 5: 2353-2370. PMID 20161005 DOI: 10.1021/ct900242e  1
2009 Hatcher E, Guvench O, Mackerell AD. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol. Journal of Chemical Theory and Computation. 5: 1315-1327. PMID 20160980 DOI: 10.1021/ct9000608  1
2009 Priyakumar UD, Hyeon C, Thirumalai D, Mackerell AD. Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. Journal of the American Chemical Society. 131: 17759-61. PMID 19919063 DOI: 10.1021/ja905795v  1
2009 Sorci L, Pan Y, Eyobo Y, Rodionova I, Huang N, Kurnasov O, Zhong S, MacKerell AD, Zhang H, Osterman AL. Targeting NAD Biosynthesis in Bacterial Pathogens: Structure-Based Development of Inhibitors of Nicotinate Mononucleotide Adenylyltransferase NadD Chemistry and Biology. 16: 849-861. PMID 19716475 DOI: 10.1016/j.chembiol.2009.07.006  1
2009 Hatcher E, Guvench O, Mackerell AD. CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. The Journal of Physical Chemistry. B. 113: 12466-76. PMID 19694450 DOI: 10.1021/jp905496e  1
2009 Burkhard K, Smith S, Deshmukh R, MacKerell AD, Shapiro P. Development of extracellular signal-regulated kinase inhibitors. Current Topics in Medicinal Chemistry. 9: 678-89. PMID 19689374 DOI: 10.2174/156802609789044416  1
2009 Guvench O, MacKerell AD. Computational fragment-based binding site identification by ligand competitive saturation. Plos Computational Biology. 5: e1000435. PMID 19593374 DOI: 10.1371/journal.pcbi.1000435  1
2009 Charpentier TH, Wilder PT, Liriano MA, Varney KM, Zhong S, Coop A, Pozharski E, MacKerell AD, Toth EA, Weber DJ. 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. 48: 6202-12. PMID 19469484 DOI: 10.1021/bi9005754  1
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/jcc.21287  1
2009 Banavali NK, MacKerell AD. Characterizing structural transitions using localized free energy landscape analysis Plos One. 4. PMID 19436759 DOI: 10.1371/journal.pone.0005525  1
2009 González PM, Acharya C, MacKerell AD, Polli JE. Inhibition requirements of the human apical sodium-dependent bile acid transporter (hASBT) using aminopiperidine conjugates of glutamyl-bile acids Pharmaceutical Research. 26: 1665-1678. PMID 19384469 DOI: 10.1007/s11095-009-9877-3  1
2009 Harder E, Mackerell AD, Roux B. Many-body polarization effects and the membrane dipole potential. Journal of the American Chemical Society. 131: 2760-1. PMID 19199514 DOI: 10.1021/ja806825g  1
2009 Guvench O, MacKerell AD. Computational evaluation of protein-small molecule binding. Current Opinion in Structural Biology. 19: 56-61. PMID 19162472 DOI: 10.1016/j.sbi.2008.11.009  1
2009 Lopes PE, Lamoureux G, Mackerell AD. Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. Journal of Computational Chemistry. 30: 1821-38. PMID 19090564 DOI: 10.1002/jcc.21183  1
2009 MacKerell AD. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA Journal of Physical Chemistry B. 113: 3235-3244. DOI: 10.1021/jp8102782  1
2009 Lopes PEM, Demchuk E, Mackerell AD. Reconstruction of the (011) surface on α-quartz: A semiclassical ab initio molecular dynamics study International Journal of Quantum Chemistry. 109: 50-64. DOI: 10.1002/qua.21726  1
2008 Kamath G, Guvench O, MacKerell AD. CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol. Journal of Chemical Theory and Computation. 4: 765-78. PMID 26621091 DOI: 10.1021/ct800019u  1
2008 Kamath G, Guvench O, MacKerell AD. CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol. Journal of Chemical Theory and Computation. 4: 1990. PMID 26620340 DOI: 10.1021/ct800423m  1
2008 Matthews MM, Weber DJ, Shapiro PS, Coop A, Mackerell AD. Inhibition of protein-protein interactions with low molecular weight compounds. Current Trends in Medicinal Chemistry. 5: 21-32. PMID 21927717  1
2008 Mackerell AD, Shim JH, Anisimov VM. Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide. Journal of Chemical Theory and Computation. 4: 1307-1312. PMID 20445813 DOI: 10.1021/ct8000969  1
2008 Chen F, Mackerell AD, Luo Y, 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. PMID 19105050 DOI: 10.1007/s12079-008-0034-2  1
2008 Yu WM, Guvench O, Mackerell AD, Qu CK. Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. Journal of Medicinal Chemistry. 51: 7396-404. PMID 19007293 DOI: 10.1021/jm800229d  1
2008 Acharya C, Seo PR, Polli JE, MacKerell AD. Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes Molecular Pharmaceutics. 5: 818-828. PMID 18710255 DOI: 10.1021/mp800035h  1
2008 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 Journal of Medicinal Chemistry. 51: 4553-4562. PMID 18630893 DOI: 10.1021/jm8001668  1
2008 Charpentier TH, Wilder PT, Liriano MA, Varney KM, Pozharski E, MacKerell AD, Coop A, Toth EA, Weber DJ. Divalent metal ion complexes of S100B in the absence and presence of pentamidine. Journal of Molecular Biology. 382: 56-73. PMID 18602402 DOI: 10.1016/j.jmb.2008.06.047  1
2008 Guvench O, Greene SN, Kamath G, Brady JW, Venable RM, Pastor RW, Mackerell AD. Additive empirical force field for hexopyranose monosaccharides. Journal of Computational Chemistry. 29: 2543-64. PMID 18470966 DOI: 10.1002/jcc.21004  1
2008 Guvench O, MacKerell AD. Automated conformational energy fitting for force-field development. Journal of Molecular Modeling. 14: 667-79. PMID 18458967 DOI: 10.1007/s00894-008-0305-0  1
2008 Lee H, Venable RM, MacKerell AD, Pastor RW. Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy Biophysical Journal. 95: 1590-1599. PMID 18456821 DOI: 10.1529/biophysj.108.133025  1
2008 Chen X, Zhong S, Zhu X, Dziegielewska B, Ellenberger T, Wilson GM, MacKerell AD, Tomkinson AE. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair Cancer Research. 68: 3169-3177. PMID 18451142 DOI: 10.1158/0008-5472.CAN-07-6636  1
2008 Guvench O, MacKerell AD. Comparison of protein force fields for molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 443: 63-88. PMID 18446282 DOI: 10.1007/978-1-59745-177-2_4  1
2008 Harder E, Anisimov VM, Whitfield T, MacKerell AD, Roux B. Understanding the dielectric properties of liquid amides from a polarizable force field Journal of Physical Chemistry B. 112: 3509-3521. PMID 18302362 DOI: 10.1021/jp709729d  1
2008 Mackerell AD, Nilsson L. Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology. 18: 194-9. PMID 18281210 DOI: 10.1016/j.sbi.2007.12.012  1
2008 Li L, Vorobyov I, MacKerell AD, Allen TW. Is arginine charged in a membrane? Biophysical Journal. 94: L11-3. PMID 17981901 DOI: 10.1529/biophysj.107.121566  1
2008 Zhong S, MacKerell AD. Pose scaling: Geometrical assessment of ligand binding poses Journal of Theoretical and Computational Chemistry. 7: 833-852. DOI: 10.1142/S0219633608004155  1
2008 Priyakumar UD, MacKerell AD. Atomic detail investigation of the structure and dynamics of DNA·RNA hybrids: A molecular dynamics study Journal of Physical Chemistry B. 112: 1515-1524. DOI: 10.1021/jp709827m  1
2008 MacKerell AD, Shim JH, Anisimov VM. Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide Journal of Chemical Theory and Computation. 4: 1307-1312. DOI: 10.1021/ct8000969  1
2008 Klauda JB, Venable RM, MacKerell AD, Pastor RW. Chapter 1 Considerations for Lipid Force Field Development Current Topics in Membranes. 60: 1-48. DOI: 10.1016/S1063-5823(08)00001-X  1
2007 Vorobyov I, Anisimov VM, Greene S, Venable RM, Moser A, Pastor RW, MacKerell AD. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers. Journal of Chemical Theory and Computation. 3: 1120-33. PMID 26627431 DOI: 10.1021/ct600350s  1
2007 Xie W, Pu J, Mackerell AD, Gao J. Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. Journal of Chemical Theory and Computation. 3: 1878-1889. PMID 18958290 DOI: 10.1021/ct700146x  1
2007 Anisimov VM, Vorobyov IV, Roux B, Mackerell AD. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. Journal of Chemical Theory and Computation. 3: 1927-1946. PMID 18802495 DOI: 10.1021/ct700100a  1
2007 Thomas JL, Tobias DJ, Mackerell AD. Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation. The Journal of Physical Chemistry. B. 111: 12941-4. PMID 17958354 DOI: 10.1021/jp076501p  1
2007 Zhong S, Mackerell AD. Binding response: A descriptor for selecting ligand binding site on protein surfaces Journal of Chemical Information and Modeling. 47: 2303-2315. PMID 17900106 DOI: 10.1021/ci700149k  1
2007 Furci LM, Lopes P, Eakanunkul S, Zhong S, MacKerell AD, Wilks A. Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: novel antimicrobial targets. Journal of Medicinal Chemistry. 50: 3804-13. PMID 17629261 DOI: 10.1021/jm0700969  1
2007 Markowitz J, MacKerell AD, Weber DJ. A search for inhibitors of S100B, a member of the S100 family of calcium-binding proteins. Mini Reviews in Medicinal Chemistry. 7: 609-16. PMID 17584159 DOI: 10.2174/138955707780859422  1
2007 Woodcock HL, Moran D, Pastor RW, MacKerell AD, Brooks BR. Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran. Biophysical Journal. 93: 1-10. PMID 17554075 DOI: 10.1529/biophysj.106.099986  1
2007 Lopes PE, Lamoureux G, Roux B, Mackerell AD. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. The Journal of Physical Chemistry. B. 111: 2873-85. PMID 17388420 DOI: 10.1021/jp0663614  1
2007 Guvench O, Qu CK, MacKerell AD. Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft. Bmc Structural Biology. 7: 14. PMID 17378938 DOI: 10.1186/1472-6807-7-14  1
2007 Bernard D, Coop A, MacKerell AD. Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity. Journal of Medicinal Chemistry. 50: 1799-809. PMID 17367120 DOI: 10.1021/jm0612463  1
2007 Zhong S, Macias AT, MacKerell AD. Computational identification of inhibitors of protein-protein interactions. Current Topics in Medicinal Chemistry. 7: 63-82. PMID 17266596 DOI: 10.2174/156802607779318334  1
2007 Macias AT, Banavali NK, MacKerell AD. DNA bending induced by carbocyclic sugar analogs constrained to the north conformation. Biopolymers. 85: 438-49. PMID 17211887 DOI: 10.1002/bip.20673  1
2007 Anisimov VM, Vorobyov IV, Roux B, MacKerell AD. Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model Journal of Chemical Theory and Computation. 3: 1927-1946. DOI: 10.1021/ct700100a  1
2006 Harder E, Anisimov VM, Vorobyov IV, Lopes PE, Noskov SY, MacKerell AD, Roux B. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 2: 1587-97. PMID 26627029 DOI: 10.1021/ct600180x  1
2006 Priyakumar UD, MacKerell AD. Base Flipping in a GCGC Containing DNA Dodecamer:  A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS. Journal of Chemical Theory and Computation. 2: 187-200. PMID 26626393 DOI: 10.1021/ct0501957  1
2006 Chen IJ, Taneja R, Yin D, Seo PR, Young D, MacKerell AD, Polli JE. Chemical substituent effect on pyridine permeability and mechanistic insight from computational molecular descriptors. Molecular Pharmaceutics. 3: 745-55. PMID 17140262 DOI: 10.1021/mp050096+  1
2006 Chen F, Hancock CN, Macias AT, Joh J, Still K, Zhong S, MacKerell AD, Shapiro P. Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure. Bioorganic & Medicinal Chemistry Letters. 16: 6281-7. PMID 17000106 DOI: 10.1016/j.bmcl.2006.09.038  1
2006 Guvench O, Mackerell AD. Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding. The Journal of Physical Chemistry. A. 110: 9934-9. PMID 16898697 DOI: 10.1021/jp0623241  1
2006 Banavali NK, Huang N, MacKerell AD. Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. The Journal of Physical Chemistry. B. 110: 10997-1004. PMID 16771353 DOI: 10.1021/jp0561322  1
2006 Lopes PE, Murashov V, Tazi M, Demchuk E, Mackerell AD. Development of an empirical force field for silica. Application to the quartz-water interface. The Journal of Physical Chemistry. B. 110: 2782-92. PMID 16471886 DOI: 10.1021/jp055341j  1
2006 Priyakumar UD, MacKerell AD. Computational approaches for investigating base flipping in oligonucleotides. Chemical Reviews. 106: 489-505. PMID 16464016 DOI: 10.1021/cr040475z  1
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 1: 153-68. PMID 26641126 DOI: 10.1021/ct049930p  1
2005 Vorobyov IV, Anisimov VM, MacKerell AD. Polarizable empirical force field for alkanes based on the classical Drude oscillator model. The Journal of Physical Chemistry. B. 109: 18988-99. PMID 16853445 DOI: 10.1021/jp053182y  1
2005 Bernard D, Coop A, MacKerell Jr AD. Conformationally sampled pharmacophore for peptidic delta opioid ligands. Journal of Medicinal Chemistry. 48: 7773-80. PMID 16302816 DOI: 10.1021/jm050785p  1
2005 Markowitz J, Mackerell AD, Carrier F, Charpentier TH, Weber DJ. Design of Inhibitors for S100B. Current Topics in Medicinal Chemistry. 5: 1093-108. PMID 16248785 DOI: 10.2174/156802605774370865  1
2005 Habtemariam B, Anisimov VM, MacKerell AD. Cooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations. Nucleic Acids Research. 33: 4212-22. PMID 16049027 DOI: 10.1093/nar/gki724  1
2005 Hancock CN, Macias A, Lee EK, Yu SY, Mackerell AD, Shapiro P. Identification of novel extracellular signal-regulated kinase docking domain inhibitors. Journal of Medicinal Chemistry. 48: 4586-95. PMID 15999996 DOI: 10.1021/jm0501174  1
2005 Wu H, Thatcher LN, Bernard D, Parrish DA, Deschamps JR, Rice KC, MacKerell AD, Coop A. Position of coordination of the lithium ion determines the regioselectivity of demethylations of 3,4-dimethoxymorphinans with L-selectride. Organic Letters. 7: 2531-4. PMID 15957883 DOI: 10.1021/ol050433c  1
2005 Boresch S, Leitgeb M, Beselman A, MacKerell AD. Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives. Journal of the American Chemical Society. 127: 4640-8. PMID 15796529 DOI: 10.1021/ja044935h  1
2005 Wu H, Bernard D, Chen W, Strahan GD, Deschamps JR, Parrish DA, Lewis JW, MacKerell AD, Coop A. Functionalization of the 6,14-bridge of the orvinols. 2. Preparation of 18- and 19-hydroxyl-substituted thevinols and their treatment with benzyl bromide. The Journal of Organic Chemistry. 70: 1907-10. PMID 15730320 DOI: 10.1021/jo048388u  1
2005 Huang N, MacKerell AD. Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. Journal of Molecular Biology. 345: 265-74. PMID 15571720 DOI: 10.1016/j.jmb.2004.10.042  1
2004 Markowitz J, Chen I, Gitti R, Baldisseri DM, Pan Y, Udan R, Carrier F, MacKerell AD, Weber DJ. Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction. Journal of Medicinal Chemistry. 47: 5085-93. PMID 15456252 DOI: 10.1021/jm0497038  1
2004 Wymore T, Hempel J, Cho SS, Mackerell AD, Nicholas HB, Deerfield DW. Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation. Proteins. 57: 758-71. PMID 15390260 DOI: 10.1002/prot.20256  1
2004 Huang N, MacKerell AD. Atomistic view of base flipping in DNA. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 362: 1439-60. PMID 15306460 DOI: 10.1098/rsta.2004.1383  1
2004 Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Research. 32: 3877-86. PMID 15273274 DOI: 10.1093/nar/gkh701  1
2004 Patel S, Mackerell AD, Brooks CL. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. Journal of Computational Chemistry. 25: 1504-14. PMID 15224394 DOI: 10.1002/jcc.20077  1
2004 Huang N, Nagarsekar A, Xia G, Hayashi J, MacKerell AD. 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 binding site. Journal of Medicinal Chemistry. 47: 3502-11. PMID 15214778 DOI: 10.1021/jm030470e  1
2004 Mackerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Journal of Computational Chemistry. 25: 1400-15. PMID 15185334 DOI: 10.1002/jcc.20065  1
2004 Macias AT, Hernandez RJ, Mehta AK, MacKerell AD, Ticku MK, Coop A. 3-chloropropanoic acid (UMB66): a ligand for the gamma-hydroxybutyric acid receptor lacking a 4-hydroxyl group. Bioorganic & Medicinal Chemistry. 12: 1643-7. PMID 15028257 DOI: 10.1016/j.bmc.2004.01.025  1
2003 Bernard D, Coop A, MacKerell AD. 2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists. Journal of the American Chemical Society. 125: 3101-7. PMID 12617677 DOI: 10.1021/ja027644m  1
2003 Chen W, Wu H, Bernard D, Metcalf MD, Deschamps JR, Flippen-Anderson JL, MacKerell AD, Coop A. Rearrangement of 5-trimethylsilylthebaine on treatment with L-selectride: an efficient synthesis of (+)-bractazonine. The Journal of Organic Chemistry. 68: 1929-32. PMID 12608812 DOI: 10.1021/jo020704m  1
2003 Pan Y, Huang N, Cho S, MacKerell AD. Consideration of molecular weight during compound selection in virtual target-based database screening Journal of Chemical Information and Computer Sciences. 43: 267-272. PMID 12546562 DOI: 10.1021/ci020055f  1
2003 Huang N, Banavali NK, MacKerell AD. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proceedings of the National Academy of Sciences of the United States of America. 100: 68-73. PMID 12506195 DOI: 10.1073/pnas.0135427100  1
2002 Chen IJ, Neamati N, MacKerell AD. Structure-based inhibitor design targeting HIV-1 integrase. Current Drug Targets. Infectious Disorders. 2: 217-34. PMID 12462126 DOI: 10.2174/1568005023342380  1
2002 Banavali NK, MacKerell AD. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. Journal of Molecular Biology. 319: 141-60. PMID 12051942 DOI: 10.1016/S0022-2836(02)00194-8  1
2002 Foloppe N, Hartmann B, Nilsson L, MacKerell AD. Intrinsic conformational energetics associated with the glycosyl torsion in DNA: A quantum mechanical study Biophysical Journal. 82: 1554-1569. PMID 11867468  1
2001 Foloppe N, Nilsson L, MacKerell AD. Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics Biopolymers. 61: 61-76. PMID 11891629 DOI: 10.1002/1097-0282(2001)61:1<61::AID-BIP10047>3.0.CO;2-1  1
2001 Izaguirre G, Pietruszko R, Cho S, MacKerell A. Human aldehyde dehydrogenase catalytic activity and structural interactions with coenzyme analogs. Journal of Biomolecular Structure & Dynamics. 19: 429-47. PMID 11790142 DOI: 10.1080/07391102.2001.10506752  1
2001 Marquez VE, Wang P, Nicklaus MC, Maier M, Manoharan M, Christman JK, Banavali NK, Mackerell AD. Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites. Nucleosides, Nucleotides & Nucleic Acids. 20: 451-9. PMID 11563060 DOI: 10.1081/NCN-100002319  1
2001 Banavali NK, MacKerell AD. Re-examination of the intrinsic, dynamic and hydration properties of phosphoramidate DNA. Nucleic Acids Research. 29: 3219-30. PMID 11470880 DOI: 10.1093/nar/29.15.3219  1
2001 Banavali NK, MacKerell AD. Reevaluation of stereoelectronic contributions to the conformational properties of the phosphodiester and N3'-phosphoramidate moieties of nucleic acids. Journal of the American Chemical Society. 123: 6747-55. PMID 11448177  1
2000 Chen IJ, Neamati N, Nicklaus MC, Orr A, Anderson L, Barchi JJ, Kelley JA, Pommier Y, MacKerell AD. Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets. Bioorganic & Medicinal Chemistry. 8: 2385-98. PMID 11058033 DOI: 10.1016/S0968-0896(00)00180-2  1
1998 MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B. 102: 3586-616. PMID 24889800 DOI: 10.1021/jp973084f  1
1997 Li Y, MacKerell AD, Egorin MJ, Ballesteros MF, Rosen DM, Wu YY, Blamble DA, Callery PS. Comparative molecular field analysis-based predictive model of structure-function relationships of polyamine transport inhibitors in L1210 cells Cancer Research. 57: 234-239. PMID 9000561  1
1995 MacKerell AD, Sommer MS, Karplus M. pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis. Journal of Molecular Biology. 247: 774-807. PMID 7723031 DOI: 10.1006/jmbi.1994.0180  0.32
1991 MacKerell AD, Rigler R, Hahn U, Saenger W. Thermodynamic analysis of the equilibrium, association and dissociation of 2'GMP and 3'GMP with ribonuclease T1 at pH 5.3. Biochimica Et Biophysica Acta. 1073: 357-65. PMID 1849008 DOI: 10.1016/0304-4165(91)90143-5  1
1990 Abriola DP, MacKerell AD, Pietruszko R. Correlation of loss of activity of human aldehyde dehydrogenase with reaction of bromoacetophenone with glutamic acid-268 and cysteine-302 residues. Partial-sites reactivity of aldehyde dehydrogenase. The Biochemical Journal. 266: 179-87. PMID 1968743  1
1989 MacKerell AD, Nilsson L, Rigler R, Heinemann U, Saenger W. Molecular dynamics simulations of ribonuclease T1: comparison of the free enzyme and the 2' GMP-enzyme complex. Proteins. 6: 20-31. PMID 2558378 DOI: 10.1002/prot.340060103  1
1988 MacKerell AD, Nilsson L, Rigler R, Saenger W. Molecular dynamics simulations of ribonuclease T1: analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme. Biochemistry. 27: 4547-56. PMID 3139027  1
1988 MacKerell AD, Rigler R, Nilsson L, Heinemann U, Saenger W. Molecular dynamics simulations of ribonuclease T1. Effect of solvent on the interaction with 2'GMP. European Biophysics Journal : Ebj. 16: 287-97. PMID 2853669 DOI: 10.1007/BF00254065  1
1987 MacKerell AD, Pietruszko R. Chemical modification of human aldehyde dehydrogenase by physiological substrate. Biochimica Et Biophysica Acta. 911: 306-17. PMID 3814607 DOI: 10.1016/0167-4838(87)90071-9  1
1987 Abriola DP, Fields R, Stein S, MacKerell AD, Pietruszko R. Active site of human liver aldehyde dehydrogenase. Biochemistry. 26: 5679-84. PMID 3676276  1
1987 Pietruszko R, MacKerell AD. Stoichiometry of chemical modification of human aldehyde dehydrogenase: evidence for "quarter of the sites" reactivity. Progress in Clinical and Biological Research. 232: 37-52. PMID 3615426  1
1987 MacKerell AD, Rigler R, Nilsson L, Hahn U, Saenger W. Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1. Biophysical Chemistry. 26: 247-61. PMID 3111558 DOI: 10.1016/0301-4622(87)80027-3  1
1986 MacKerell AD, MacWright RS, Pietruszko R. Bromoacetophenone as an affinity reagent for human liver aldehyde dehydrogenase. Biochemistry. 25: 5182-9. PMID 3768340  1
1986 MacKerell AD, Blatter EE, Pietruszko R. Human aldehyde dehydrogenase: kinetic identification of the isozyme for which biogenic aldehydes and acetaldehyde compete. Alcoholism, Clinical and Experimental Research. 10: 266-70. PMID 3526948  1
1985 Pietruszko R, MacKerell AD, Ferencz-Biro K. Adducts of propiolaldehyde and 3,4-dihydroxyphenylacetaldehyde with human aldehyde dehydrogenase. Progress in Clinical and Biological Research. 183: 67-74. PMID 4048184  1
1985 Pietruszko R, Ferencz-Biro K, MacKerell AD. Chemical modification of human aldehyde dehydrogenase. Progress in Clinical and Biological Research. 174: 29-41. PMID 3983204  1
1985 MacKerell AD, Vallari RC, Pietruszko R. Human mitochondrial aldehyde dehydrogenase inhibition by diethyldithiocarbamic acid methanethiol mixed disulfide: a derivative of disulfiram. Febs Letters. 179: 77-81. PMID 2981182 DOI: 10.1016/0014-5793(85)80195-2  1
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