Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, B(I) and B(II) forms of duplex DNA

Por MacKerell, Alexander D.
Publicado em 2009

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

Por Pan, Yongping, MacKerell, Alexander D.
Publicado em 2003

Computational evaluation of protein – small molecule binding

Por Guvench, Olgun, MacKerell, Alexander D.
Publicado em 2009

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Por Guvench, Olgun, MacKerell, Alexander D.
Publicado em 2009

Automated conformational energy fitting for force-field development

Por Guvench, Olgun, MacKerell, Alexander D.
Publicado em 2008

Molecular dynamics simulations of nucleic acid-protein complexes

Por MacKerell, Alexander D., Nilsson, Lennart
Publicado em 2008

Polarizable Empirical Force Field for Sulfur-Containing Compounds Based on the Classical Drude Oscillator Model

Por Zhu, Xiao, MacKerell, Alexander D.
Publicado em 2010

Computational ligand-based rational design: Role of conformational sampling and force fields in model development

Por Shim, Jihyun, MacKerell, Alexander D.
Publicado em 2011

Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides

Por Mallajosyula, Sairam S., MacKerell, Alexander D.
Publicado em 2011

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Por Huang, Jing, MacKerell, Alexander D.
Publicado em 2013

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

Por Savelyev, Alexey, MacKerell, Alexander D.
Publicado em 2014

All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

Por Savelyev, Alexey, MacKerell, Alexander D.
Publicado em 2014

Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)(3) Peptide

Por Huang, Jing, MacKerell, Alexander D.
Publicado em 2014

Differential Impact of the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) on DNA Conformational Properties

Por Savelyev, Alexey, MacKerell, Alexander D.
Publicado no J Phys Chem Lett (2014)

Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM)

Por Yang, Mingjun, MacKerell, Alexander D.
Publicado no J Chem Theory Comput (2015)

Competition among Li(+), Na(+), K(+) and Rb(+) Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

Por Savelyev, Alexey, MacKerell, Alexander D.
Publicado no J Phys Chem B (2015)

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

Por Jana, Madhurima, MacKerell, Alexander D.
Publicado no J Phys Chem B (2015)

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 Hyd...

Por Savelyev, Alexey, MacKerell, Alexander D.
Publicado no J Chem Theory Comput (2015)

Computer-Aided Drug Design Methods

Por Yu, Wenbo, MacKerell, Alexander D.
Publicado no Methods Mol Biol (2017)

Re-examination of the intrinsic, dynamic and hydration properties of phosphoramidate DNA

Por Banavali, Nilesh K., MacKerell, Alexander D.
Publicado em 2001