Charles L Brooks

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Charles L Brooks

Publications by authors named "Charles L Brooks"

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100Publications

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Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics.

J Phys Chem Lett 2018 Jun 6;9(12):3328-3332. Epub 2018 Jun 6.

Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.

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June 2018

Molecular interactions between single layered MoS and biological molecules.

Chem Sci 2018 Feb 30;9(7):1769-1773. Epub 2017 Nov 30.

Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , USA . Email:

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February 2018

CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.

J Comput Aided Mol Des 2018 01 7;32(1):89-102. Epub 2017 Sep 7.

Department of Computational Medicine and Bioinformatics, Univeristy of Michigan, Ann Arbor, MI, 48109, USA.

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January 2018

Effect of immobilization site on the orientation and activity of surface-tethered enzymes.

Phys Chem Chem Phys 2018 Jan;20(2):1021-1029

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

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January 2018

Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time.

J Biol Chem 2017 09 24;292(36):14963-14976. Epub 2017 Jul 24.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055

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September 2017

Tuning RNA folding and function through rational design of junction topology.

Nucleic Acids Res 2017 09;45(16):9706-9715

Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA.

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September 2017

A rapid solvent accessible surface area estimator for coarse grained molecular simulations.

J Comput Chem 2017 Jun 16;38(15):1270-1274. Epub 2017 Apr 16.

Departments of Biophysics and Chemistry, University of Michigan, Ann Arbor, MI, 48109.

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June 2017

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

J Comput Chem 2017 Jun 11;38(21):1879-1886. Epub 2017 May 11.

Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.

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June 2017

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

J Chem Theory Comput 2017 Jun 26;13(6):2501-2510. Epub 2017 May 26.

Department of Computational Medicine & Bioinformatics, ‡Department of Chemistry, §Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States.

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June 2017

Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models.

Small 2017 May 7;13(18). Epub 2017 Mar 7.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.

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May 2017

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.

J Phys Chem B 2017 04 10;121(15):3626-3635. Epub 2017 Feb 10.

Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.

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April 2017

Mechanism of Vps4 hexamer function revealed by cryo-EM.

Sci Adv 2017 Apr 14;3(4):e1700325. Epub 2017 Apr 14.

Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.

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April 2017

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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December 2016

A Synthetic Loop Replacement Peptide That Blocks Canonical NF-κB Signaling.

Angew Chem Int Ed Engl 2016 Nov 28;55(48):14997-15001. Epub 2016 Oct 28.

Department of Chemistry, University of Michigan, Ann Arbor, USA.

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November 2016

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:

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October 2016

Efficient implementation of constant pH molecular dynamics on modern graphics processors.

J Comput Chem 2016 09 12;37(24):2171-80. Epub 2016 Jul 12.

Department of Chemistry and Biophysics Program, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109.

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September 2016

Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.

J Am Chem Soc 2016 08 2;138(31):9826-39. Epub 2016 Aug 2.

Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.

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August 2016

Visualizing chaperone-assisted protein folding.

Nat Struct Mol Biol 2016 07 30;23(7):691-7. Epub 2016 May 30.

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.

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July 2016

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.

J Comput Chem 2016 Apr 20;37(10):927-39. Epub 2016 Jan 20.

Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109.

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April 2016

Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.

J Comput Chem 2016 Mar 6;37(6):587-94. Epub 2015 Aug 6.

Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, 48109.

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March 2016

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.

J Comput Chem 2016 Mar 21;37(8):753-62. Epub 2015 Dec 21.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan.

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March 2016

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.

Nucleic Acids Res 2016 Jan 19;44(1):402-12. Epub 2015 Oct 19.

Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA

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January 2016

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.

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January 2016

Editorial.

Protein Sci 2016 Jan;25(1):5-8

Department of Medicinal Chemistry, and Pharmacology Purdue University, West Lafayette, IN, 47907.

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January 2016

Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature.

Phys Rev E 2016 Jan 28;93(1):012417. Epub 2016 Jan 28.

Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA.

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January 2016

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:

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November 2015

Regulation of calreticulin-major histocompatibility complex (MHC) class I interactions by ATP.

Proc Natl Acad Sci U S A 2015 Oct 29;112(41):E5608-17. Epub 2015 Sep 29.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109;

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October 2015

Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ.

J Am Chem Soc 2015 Aug 11;137(32):10190-8. Epub 2015 Aug 11.

†Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.

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August 2015

Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces.

Langmuir 2015 Jun 27;31(22):6145-53. Epub 2015 May 27.

†Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States.

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June 2015

Accurate modeling of ionic surfactants at high concentration.

J Phys Chem B 2015 May 7;119(20):6217-24. Epub 2015 May 7.

†Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States.

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May 2015

Multiscale modeling of a conditionally disordered pH-sensing chaperone.

J Mol Biol 2015 Apr 10;427(8):1670-80. Epub 2015 Jan 10.

Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

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April 2015

CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

J Struct Biol 2015 Apr 16;190(1):47-55. Epub 2015 Feb 16.

Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

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April 2015

Membrane environment modulates the pKa values of transmembrane helices.

J Phys Chem B 2015 Apr 22;119(13):4601-7. Epub 2015 Mar 22.

†Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States.

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April 2015

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

Proteins 2015 Mar 21;83(3):403-410. Epub 2015 Jan 21.

Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan, Ann Arbor MI 48109 USA.

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March 2015

pH-dependent transient conformational states control optical properties in cyan fluorescent protein.

J Am Chem Soc 2015 Mar 18;137(8):2892-900. Epub 2015 Feb 18.

Department of Chemistry and ‡Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States.

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March 2015

Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

J Am Chem Soc 2015 Mar 9;137(10):3592-9. Epub 2015 Mar 9.

∥Departments of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.

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March 2015

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations.

J Chem Theory Comput 2015 Mar;11(3):1267-77

Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States.

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March 2015

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces.

BMC Bioinformatics 2015 Feb 1;16:33. Epub 2015 Feb 1.

Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA.

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February 2015

Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion.

Proc Natl Acad Sci U S A 2015 Feb 2;112(7):2034-9. Epub 2015 Feb 2.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, MI 48109; and

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February 2015

Hierarchy of RNA functional dynamics.

Annu Rev Biochem 2014 5;83:441-66. Epub 2014 Mar 5.

Departments of 1Biophysics and.

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January 2015

Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models.

J Chem Theory Comput 2015 Jan;11(1):325-31

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States

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January 2015

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.

Nucleic Acids Res 2014 Oct 12;42(18):11792-804. Epub 2014 Sep 12.

Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC 27710, USA

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October 2014

A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA.

J Phys Chem B 2014 Oct 15;118(42):12168-75. Epub 2014 Oct 15.

Department of Chemistry and Biophysics, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States.

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October 2014

Environmental effect on surface immobilized biological molecules.

J Phys Chem B 2014 Oct 14;118(42):12176-85. Epub 2014 Oct 14.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Si Pai Lou 2, Nanjing 210096, China.

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October 2014

Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins.

J Phys Chem Lett 2014 Oct 19;5(19):3441-3444. Epub 2014 Sep 19.

Department of Chemistry and Biophysics Program, The University of Michigan , Ann Arbor, Michigan 48109, United States.

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October 2014

Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.

Nucleic Acids Res 2014 Oct 7;42(19):12126-37. Epub 2014 Oct 7.

Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA Department of Biophysics, University of Michigan, 930 N University, Ann Arbor, MI 48109, USA

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October 2014

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

J Mol Biol 2014 Sep 9;426(19):3201-3213. Epub 2014 May 9.

Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA. Electronic address:

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September 2014

PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements.

J Comput Chem 2014 Sep 4;35(24):1757-61. Epub 2014 Jul 4.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109; Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, Fax: +1 (734) 647 1604.

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September 2014

Prepaying the entropic cost for allosteric regulation in KIX.

Proc Natl Acad Sci U S A 2014 Aug 7;111(33):12067-72. Epub 2014 Jul 7.

Departments of Chemistry andBiophysics, and

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August 2014

Quantifying chaperone-mediated transitions in the proteostasis network of E. coli.

PLoS Comput Biol 2013 14;9(11):e1003324. Epub 2013 Nov 14.

Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, United States of America.

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July 2014

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

Proteins 2014 Jul 15;82(7):1319-31. Epub 2014 Jan 15.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109.

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July 2014

Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes.

J Phys Chem B 2014 Jul 29;118(28):8118-27. Epub 2014 May 29.

Department of Chemistry and ‡Biophysics Program, University of Michigan , 930 N. University Avenue , Ann Arbor, Michigan 48109-1055, USA.

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July 2014

Modulation of frustration in folding by sequence permutation.

Proc Natl Acad Sci U S A 2014 Jul 7;111(29):10562-7. Epub 2014 Jul 7.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605;

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July 2014

From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation.

Comput Struct Biotechnol J 2012 30;2:e201209018. Epub 2012 Nov 30.

University of Michigan, Department of Chemistry and Biophysics, 930 North University Avenue, Ann Arbor, MI 48109 USA.

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June 2014

Uncovering pH-dependent transient states of proteins with buried ionizable residues.

J Am Chem Soc 2014 Jun 3;136(24):8496-9. Epub 2014 Jun 3.

Department of Chemistry and ‡Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States.

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June 2014

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.

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May 2014

WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.

J Phys Chem B 2014 Apr 11;118(13):3532-42. Epub 2014 Feb 11.

Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States.

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April 2014

Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation.

J Struct Biol 2014 Mar 19;185(3):375-82. Epub 2013 Dec 19.

Health Science Research Facility 130, 149 Beaumont Avenue, Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT 05405, United States.

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March 2014

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges.

J Phys Chem B 2014 Mar 3;118(10):2615-27. Epub 2014 Mar 3.

Departments of Biophysics and ‡Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States.

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March 2014

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.

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March 2014

pH-induced stability switching of the bacteriophage HK97 maturation pathway.

J Am Chem Soc 2014 Feb 13;136(8):3097-107. Epub 2014 Feb 13.

Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269, United States.

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February 2014

Crowding induced collective hydration of biological macromolecules over extended distances.

J Am Chem Soc 2014 Jan 16;136(1):188-94. Epub 2013 Dec 16.

Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States.

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January 2014

Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase.

Top Curr Chem 2013 ;337:165-87

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.

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December 2013

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.

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December 2013

Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule.

ACS Chem Biol 2013 Dec 24;8(12):2778-84. Epub 2013 Oct 24.

Department of Chemical Engineering, University of New Hampshire , Durham, New Hampshire 03824, United States of America.

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December 2013

Viral capsid proteins are segregated in structural fold space.

PLoS Comput Biol 2013 7;9(2):e1002905. Epub 2013 Feb 7.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

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October 2013

Binding and folding of the small bacterial chaperone HdeA.

J Phys Chem B 2013 Oct 1;117(42):13219-25. Epub 2013 Jul 1.

Department of Chemistry, The University of Michigan , Ann Arbor, Michigan, United States.

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October 2013

Deconstructing activation events in rhodopsin.

J Am Chem Soc 2013 Jul 22;135(30):10906-9. Epub 2013 Jul 22.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

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July 2013

A universal trend among proteomes indicates an oily last common ancestor.

PLoS Comput Biol 2012 27;8(12):e1002839. Epub 2012 Dec 27.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America.

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May 2013

pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability.

Protein Sci 2013 May 30;22(5):595-604. Epub 2013 Mar 30.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, USA.

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May 2013

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

J Am Chem Soc 2013 May 29;135(18):6766-9. Epub 2013 Apr 29.

Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States.

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May 2013

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.

J Comput Chem 2013 Apr 7;34(11):893-903. Epub 2013 Jan 7.

Department of Chemistry & Department of Biophysics University of Michigan, 930 N. University Ave. Ann Arbor, MI 48109 USA

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April 2013

Chaperone activation by unfolding.

Proc Natl Acad Sci U S A 2013 Apr 4;110(14):E1254-62. Epub 2013 Mar 4.

Howard Hughes Medical Institute and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA.

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April 2013

Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.

J Phys Chem B 2013 Apr 1;117(14):3738-46. Epub 2013 Apr 1.

Department of Chemistry and Biophysics Program, Department of Biological Chemistry, and Biophysics Program, University of Michigan , Ann Arbor, Michigan, USA.

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April 2013

Ordering a dynamic protein via a small-molecule stabilizer.

J Am Chem Soc 2013 Mar 22;135(9):3363-6. Epub 2013 Feb 22.

Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.

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March 2013

Native states of fast-folding proteins are kinetic traps.

J Am Chem Soc 2013 Mar 15;135(12):4729-34. Epub 2013 Mar 15.

Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109, USA.

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March 2013

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.

J Phys Chem Lett 2013 Mar 12;4(5):760-766. Epub 2013 Feb 12.

Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States.

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March 2013

pH-dependent dynamics of complex RNA macromolecules.

J Chem Theory Comput 2013 Feb 3;9(2):935-943. Epub 2013 Jan 3.

Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States.

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February 2013

Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase.

J Am Chem Soc 2012 Sep 7;134(37):15357-70. Epub 2012 Sep 7.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.

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September 2012

Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps.

Structure 2012 Sep;20(9):1453-62

Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Chem 2006, Ann Arbor, MI 48109, USA.

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September 2012

Molecular mechanisms of prolactin and its receptor.

Authors:
Charles L Brooks

Endocr Rev 2012 Aug 10;33(4):504-25. Epub 2012 May 10.

Departments of Veterinary Biosciences and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.

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August 2012

On the morphology of viral capsids: elastic properties and buckling transitions.

J Phys Chem B 2012 Jul 27;116(29):8604-9. Epub 2012 Mar 27.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.

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July 2012

Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents.

J Phys Chem B 2012 May 7;116(19):5604-11. Epub 2012 May 7.

Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States.

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May 2012

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.

Nucleic Acids Res 2012 Feb 18;40(3):1345-55. Epub 2011 Oct 18.

Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA.

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February 2012

Mechanics of bacteriophage maturation.

Proc Natl Acad Sci U S A 2012 Feb 30;109(7):2342-7. Epub 2012 Jan 30.

Natuur- en Sterrenkunde and LaserLab, VU University, 1081 HV Amsterdam, The Netherlands.

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February 2012

Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways.

Biophys J 2012 Feb 7;102(3):606-12. Epub 2012 Feb 7.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA.

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February 2012

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.

Nucleic Acids Res 2012 Jan 21;40(2):892-904. Epub 2011 Sep 21.

Departments of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.

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January 2012

MATCH: an atom-typing toolset for molecular mechanics force fields.

J Comput Chem 2012 Jan 1;33(2):189-202. Epub 2011 Nov 1.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, USA.

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January 2012

Quantifying hub-like behavior in protein folding networks.

J Chem Theory Comput 2012 ;8(9):3044-3052

Department of Chemistry, The University of Michigan, Ann Arbor, MI, and Department of Chemistry and Biophysics Program, The University of Michigan, Ann Arbor, MI.

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January 2012

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.

J Chem Theory Comput 2012 Jan;8(1):36-46

Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States.

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January 2012

Applying efficient implicit nongeometric constraints in alchemical free energy simulations.

J Comput Chem 2011 Dec 14;32(16):3423-32. Epub 2011 Sep 14.

Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA.

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December 2011

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics.

Proteins 2011 Dec 15;79(12):3276-86. Epub 2011 Oct 15.

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA.

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December 2011

Probing pH-dependent dissociation of HdeA dimers.

J Am Chem Soc 2011 Dec 9;133(48):19393-8. Epub 2011 Nov 9.

Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, USA.

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December 2011

The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture.

J Am Chem Soc 2011 Dec 23;133(50):20072-5. Epub 2011 Nov 23.

Department of Chemistry, University of Michigan, 930 North University, Ann Arbor, Michigan 48109, USA.

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December 2011

A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function.

Mol Inform 2011 Oct 10;30(10):896-906. Epub 2011 Oct 10.

Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA.

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October 2011

Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.

Science 2011 Sep 11;333(6048):1449-53. Epub 2011 Aug 11.

Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA.

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September 2011

3D maps of RNA interhelical junctions.

Nat Protoc 2011 Sep 15;6(10):1536-45. Epub 2011 Sep 15.

Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, Michigan, USA.

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September 2011

Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies.

J Chem Theory Comput 2011 Sep;7(9):2728-2739

Department of Chemistry & Department of Biophysics. University of Michigan. 930 N. University Ave. Ann Arbor, MI 48109 USA.

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September 2011