Search Results - "MacKerell, A. D"

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing by Vanommeslaeghe, K, MacKerell, A. D

“…Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological…”
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Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges by Vanommeslaeghe, K, Raman, E. Prabhu, MacKerell, A. D

“…Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these…”
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Development of the CHARMM Force Field for Lipids by Pastor, R. W, MacKerell, A. D

“…The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990s to the most recent version (C36) published in 2010…”
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CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields by Vanommeslaeghe, K, Hatcher, E, Acharya, C, Kundu, S, Zhong, S, Shim, J, Darian, E, Guvench, O, Lopes, P, Vorobyov, I, Mackerell, A.D. Jr

“…The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an…”
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CHARMM additive and polarizable force fields for biophysics and computer-aided drug design by Vanommeslaeghe, K., MacKerell, A.D.

“…Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it…”
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CHARMM: The biomolecular simulation program by 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

“…CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three…”
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Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies by 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, A D, Kelleher, N L, Licht, J D, Popovic, R

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Targeting of an Interrupted Polypurine:Polypyrimidine Sequence in Mammalian Cells by a Triplex-Forming Oligonucleotide Containing a Novel Base Analogue by Semenyuk, A, Darian, E, Liu, J, Majumdar, A, Cuenoud, B, Miller, P. S, MacKerell, A. D, Seidman, M. M

“…The DNA triple helix consists of a third strand of nucleic acid lying in the major groove of an intact DNA duplex. The most stable triplexes form on…”
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins by MacKerell, A. D, Bashford, D, Bellott, M, Dunbrack, R. L, Evanseck, J. D, Field, M. J, Fischer, S, Gao, J, Guo, H, Ha, S, Joseph-McCarthy, D, Kuchnir, L, Kuczera, K, Lau, F. T. K, Mattos, C, Michnick, S, Ngo, T, Nguyen, D. T, Prodhom, B, Reiher, W. E, Roux, B, Schlenkrich, M, Smith, J. C, Stote, R, Straub, J, Watanabe, M, Wiórkiewicz-Kuczera, J, Yin, D, Karplus, M

“…New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent…”
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New insights into the structure of abasic DNA from molecular dynamics simulations by Barsky, D, Foloppe, N, Ahmadia, S, Wilson, 3rd, D M, MacKerell, Jr, A D

“…Abasic (AP) sites constitute a common form of DNA damage, arising from the spontaneous or enzymatic breakage of the N-glycosyl bond and the loss of a…”
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Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads by MacKerell, Jr, A D, Lee, G U

“…The end-to-end stretching of a duplex DNA oligonucleotide has been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD)…”
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Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies by Feller, S.E., Yin, D., Pastor, R.W., MacKerell, A.D.

“…A potential energy function for unsaturated hydrocarbons is proposed and is shown to agree well with experiment, using molecular dynamics simulations of a…”
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Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3‘-Phosphoramidate Moieties of Nucleic Acids by Banavali, Nilesh K, MacKerell, Alexander D

“…The anomeric effect in the phosphodiester backbone of nucleic acids is a stereoelectronic effect that has conventionally been linked to interactions between…”
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Intrinsic Conformational Properties of Deoxyribonucleosides: Implicated Role for Cytosine in the Equilibrium Among the A, B, and Z Forms of DNA by Foloppe, Nicolas, MacKerell, Alexander D.

“…Structural properties of biomolecules are dictated by their intrinsic conformational energetics in combination with environmental contributions. Calculations…”
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Fundamental, Binary Combination, and Overtone Modes in Methoxy Adsorbed on Cu(100):  Infrared Spectroscopy and Ab Initio Calculations by Andersson, M. P, Uvdal, P, MacKerell, A. D

“…Using surface infrared absorption spectroscopy, we have measured and assigned the vibrational spectra of six different methoxy isotopomers adsorbed on a…”
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Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics by Foloppe, Nicolas, Nilsson, Lennart, MacKerell Jr, Alexander D.

“…In recent years, the use of high‐level ab initio calculations has allowed for the intrinsic conformational properties of nucleic acid building blocks to be…”
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Development and current status of the CHARMM force field for nucleic acids by MacKerell Jr, Alexander D., Banavali, Nilesh, Foloppe, Nicolas

“…The CHARMM27 all‐atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field…”
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Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium by Hart, Katarina, Foloppe, Nicolas, Baker, Christopher M, Denning, Elizabeth J, Nilsson, Lennart, MacKerell, Alexander D

“…The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles ε and ζ (BI = ε–ζ < 0 and…”
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Vibrational spectrum of methoxy adsorbed on metal surfaces: ab initio calculations and experiments by Uvdal, P., MacKerell, A.D.

“…Ab initio electronic structure calculations are used to assign the vibrational spectra of methoxy adsorbed on Mo(110). Methoxy with two different orientations…”
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Progress toward Chemical Accuracy in the Computer Simulation of Condensed Phase Reactions by Bash, Paul A., Ho, L. Lawrence, MacKerell, Alexander D., Levine, David, Hallstrom, Philip

“…We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process…”
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