Publications by authors named "Charles L Brooks"

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
J Chem Theory Comput 2016 Jan 3;12(1):405-13. Epub 2015 Dec 3.
Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States.

Protein-Protein Interfaces in Viral Capsids Are Structurally Unique.
J Mol Biol 2015 Nov 12;427(22):3613-3624. Epub 2015 Sep 12.
Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109-2218, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA. Electronic address:

Molecular structures of C- and N-terminus cysteine modified cecropin P1 chemically immobilized onto maleimide-terminated self-assembled monolayers investigated by molecular dynamics simulation.
J Phys Chem B 2014 May 16;118(21):5670-80. Epub 2014 May 16.
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Si Pai Lou 2, Nanjing 210096, China.

Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini.
J Phys Chem B 2014 Mar 6;118(11):2904-12. Epub 2014 Mar 6.
Department of Chemistry, ‡Department of Biophysics, and §Department of Environmental Health Sciences, University of Michigan , Ann Arbor, Michigan 48109, United States.

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.
Nucleic Acids Res 2013 Dec 3;41(22):10462-75. Epub 2013 Sep 3.
Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA.


Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions.
Bioorg Med Chem 2016 10 18;24(20):4812-4825. Epub 2016 Jun 18.
Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, United States. Electronic address:

Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).
ACS Chem Biol 2016 12 31;11(12):3374-3382. Epub 2016 Oct 31.
Program in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences Institute, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States.

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