| Year |
Citation |
Score |
| 2020 |
Kognole AA, Aytenfisu AH, MacKerell AD. Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides. Journal of Molecular Modeling. 26: 152. PMID 32447472 DOI: 10.1007/s00894-020-04399-0 |
0.792 |
|
| 2019 |
Kumar A, Yoluk O, MacKerell AD. FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules. Journal of Computational Chemistry. PMID 31886576 DOI: 10.1002/jcc.26138 |
0.804 |
|
| 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 |
0.767 |
|
| 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 |
0.657 |
|
| 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 |
0.326 |
|
| 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 |
0.353 |
|
| 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 |
0.654 |
|
| 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 |
0.317 |
|
| 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 |
0.343 |
|
| 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 |
0.331 |
|
| 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 |
0.355 |
|
| 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 |
0.608 |
|
| 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 |
0.336 |
|
| 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 |
0.681 |
|
| 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 |
0.665 |
|
| 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 |
0.594 |
|
| 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 |
0.647 |
|
| 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 |
0.331 |
|
| 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 |
0.468 |
|
| 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 |
0.729 |
|
| 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 |
0.301 |
|
| 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 |
0.604 |
|
| 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 |
0.508 |
|
| 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 |
0.663 |
|
| 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 |
0.695 |
|
| 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 |
0.631 |
|
| 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 |
0.79 |
|
| 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 |
0.627 |
|
| 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 |
0.324 |
|
| 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 |
0.304 |
|
| 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 |
0.645 |
|
| 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 |
0.806 |
|
| 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 |
0.673 |
|
| 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 |
0.608 |
|
| 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 |
0.678 |
|
| 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 |
0.325 |
|
| 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 |
0.791 |
|
| 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 |
0.649 |
|
| 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 |
0.796 |
|
| 2014 |
Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Current Pharmaceutical Design. 20: 3281-92. PMID 23947650 DOI: 10.2174/13816128113199990600 |
0.689 |
|
| 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 |
0.341 |
|
| 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 |
0.612 |
|
| 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 |
0.762 |
|
| 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 |
0.339 |
|
| 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 |
0.642 |
|
| 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 |
0.781 |
|
| 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 |
0.309 |
|
| 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 |
0.618 |
|
| 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 |
0.323 |
|
| 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 |
0.318 |
|
| 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 |
0.321 |
|
| 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 |
0.8 |
|
| 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 |
0.663 |
|
| 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 |
0.625 |
|
| 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 |
0.483 |
|
| 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 |
0.809 |
|
| 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 |
0.616 |
|
| 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 |
0.807 |
|
| 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 |
0.584 |
|
| 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 |
0.483 |
|
| 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 |
0.683 |
|
| 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 |
0.668 |
|
| 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 |
0.646 |
|
| 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 |
0.325 |
|
| 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 |
0.614 |
|
| 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 |
0.71 |
|
| 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 |
0.641 |
|
| 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 |
0.664 |
|
| 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 |
0.347 |
|
| 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 |
0.682 |
|
| 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 |
0.713 |
|
| 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 |
0.676 |
|
| 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 |
0.696 |
|
| 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 |
0.683 |
|
| 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 |
0.65 |
|
| 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 |
0.684 |
|
| 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 |
0.643 |
|
| 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 |
0.661 |
|
| 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 |
0.661 |
|
| 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 |
0.65 |
|
| 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 |
0.707 |
|
| 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 |
0.667 |
|
| 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 |
0.707 |
|
| 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 |
0.48 |
|
| 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 |
0.661 |
|
| 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 |
0.668 |
|
| 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 |
0.334 |
|
| 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 |
0.668 |
|
| 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 |
0.749 |
|
| 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 |
0.643 |
|
| 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 |
0.595 |
|
| 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 |
0.587 |
|
| 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 |
0.606 |
|
| 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 |
0.749 |
|
| 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 |
0.527 |
|
| 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 |
0.584 |
|
| 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 |
0.544 |
|
| 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 |
0.666 |
|
| 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 |
0.74 |
|
| 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 |
0.663 |
|
| 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 DOI: 10.1016/S0006-3495(02)75507-0 |
0.435 |
|
| 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 |
0.453 |
|
| 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 |
0.68 |
|
| 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 |
0.645 |
|
| 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 |
0.646 |
|
| 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 DOI: 10.1021/JA010295W |
0.651 |
|
| 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 |
0.496 |
|
| 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: 10.1016/S0022-2836(05)80155-X |
0.448 |
|
| 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 |
0.491 |
|
| 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 |
0.56 |
|
| 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 |
0.615 |
|
| 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 DOI: 10.1021/Bi00412A049 |
0.632 |
|
| 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 |
0.617 |
|
| 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 |
0.565 |
|
| 1987 |
Abriola DP, Fields R, Stein S, MacKerell AD, Pietruszko R. Active site of human liver aldehyde dehydrogenase. Biochemistry. 26: 5679-84. PMID 3676276 DOI: 10.1021/bi00392a015 |
0.547 |
|
| 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 |
0.524 |
|
| 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 |
0.592 |
|
| 1986 |
MacKerell AD, MacWright RS, Pietruszko R. Bromoacetophenone as an affinity reagent for human liver aldehyde dehydrogenase. Biochemistry. 25: 5182-9. PMID 3768340 |
0.556 |
|
| 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 DOI: 10.1111/j.1530-0277.1986.tb05087.x |
0.512 |
|
| 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 |
0.499 |
|
| 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 |
0.515 |
|
| 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 |
0.53 |
|
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