Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
Hart, Katarina, Foloppe, Nicolas, Baker, Christopher M, Denning, Elizabeth J, Nilsson, Lennart, MacKerell, Alexander D
Published in Journal of chemical theory and computation (10.01.2012)
Published in Journal of chemical theory and computation (10.01.2012)
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Journal Article
Development and Current Status of the CHARMM Force Field for Nucleic Acids
MacKerell, AD Jr, Banavali, N, Foloppe, N
Published in Biopolymers (Nucleic Acid Sciences) (01.01.2001)
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Published in Biopolymers (Nucleic Acid Sciences) (01.01.2001)
Journal Article
Protein-Facilitated Base Flipping in DNA by Cytosine-5-Methyltransferase
Huang, Niu, Banavali, Nilesh K., MacKerell, Alexander D.
Published in Proceedings of the National Academy of Sciences - PNAS (07.01.2003)
Published in Proceedings of the National Academy of Sciences - PNAS (07.01.2003)
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Journal Article
New insights into the structure of abasic DNA from molecular dynamics simulations
Barsky, D, Foloppe, N, Ahmadia, S, Wilson, 3rd, D M, MacKerell, Jr, A D
Published in Nucleic acids research (01.07.2000)
Published in Nucleic acids research (01.07.2000)
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Journal Article
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
Denning, Elizabeth J., Priyakumar, U. Deva, Nilsson, Lennart, Mackerell Jr, Alexander D.
Published in Journal of computational chemistry (15.07.2011)
Published in Journal of computational chemistry (15.07.2011)
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Journal Article
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
Mackerell, Alexander D., Feig, Michael, Brooks, Charles L.
Published in Journal of computational chemistry (01.08.2004)
Published in Journal of computational chemistry (01.08.2004)
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Journal Article
CHARMM: The biomolecular simulation program
Brooks, B.R, Brooks, C.L. III, Mackerell, A.D. Jr, Nilsson, L, Petrella, R.J, Roux, B, Won, Y, Archontis, G, Bartels, C, Boresch, S, Caflisch, A, Caves, L, Cui, Q, Dinner, A.R, Feig, M, Fischer, S, Gao, J, Hodoscek, M, Im, W, Kuczera, K, Lazaridis, T, Ma, J, Ovchinnikov, V, Paci, E, Pastor, R.W, Post, C.B, Pu, J.Z, Schaefer, M, Tidor, B, Venable, R.M, Woodcock, H.L, Wu, X, Yang, W, York, D.M, Karplus, M
Published in Journal of computational chemistry (30.07.2009)
Published in Journal of computational chemistry (30.07.2009)
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Journal Article
A polarizable model of water for molecular dynamics simulations of biomolecules
Lamoureux, Guillaume, Harder, Edward, Vorobyov, Igor V., Roux, Benoît, MacKerell, Alexander D.
Published in Chemical physics letters (01.01.2006)
Published in Chemical physics letters (01.01.2006)
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Journal Article
Molecular dynamics simulations of nucleic acid–protein complexes
MacKerell, Alexander D, Nilsson, Lennart
Published in Current opinion in structural biology (01.04.2008)
Published in Current opinion in structural biology (01.04.2008)
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Journal Article
Improved Treatment of the Protein Backbone in Empirical Force Fields
MacKerell, Alexander D, Feig, Michael, Brooks, Charles L
Published in Journal of the American Chemical Society (28.01.2004)
Published in Journal of the American Chemical Society (28.01.2004)
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Journal Article
Biomolecular dynamics in the 21st century
Brooks, 3rd, Charles L, MacKerell, Jr, Alexander D, Post, Carol B, Nilsson, Lennart
Published in Biochimica et biophysica acta. General subjects (01.02.2024)
Published in Biochimica et biophysica acta. General subjects (01.02.2024)
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Journal Article
Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies
Oyer, J A, Huang, X, Zheng, Y, Shim, J, Ezponda, T, Carpenter, Z, Allegretta, M, Okot-Kotber, C I, Patel, J P, Melnick, A, Levine, R L, Ferrando, A, Mackerell, Jr, A D, Kelleher, N L, Licht, J D, Popovic, R
Published in Leukemia (01.01.2014)
Published in Leukemia (01.01.2014)
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Journal Article
An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids
Feller, Scott E, MacKerell, Alexander D
Published in The journal of physical chemistry. B (10.08.2000)
Published in The journal of physical chemistry. B (10.08.2000)
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Journal Article