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Structural Basis of VHH mediated neutralization of the foodborne pathogen Listeria monocytogenes.

Toride King M, Huh I, Shenai A, Brooks TM, Brooks CL.

J Biol Chem. 2018 Jul 5. pii: jbc.RA118.003888. doi: 10.1074/jbc.RA118.003888. [Epub ahead of print]


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

Vilseck JZ, Armacost KA, Hayes RL, Goh GB, Brooks CL 3rd.

J Phys Chem Lett. 2018 Jun 21;9(12):3328-3332. doi: 10.1021/acs.jpclett.8b01284. Epub 2018 Jun 6.


Epitope Mapping of Antibody-Antigen Interactions with X-Ray Crystallography.

Toride King M, Brooks CL.

Methods Mol Biol. 2018;1785:13-27. doi: 10.1007/978-1-4939-7841-0_2.


Molecular interactions between single layered MoS2 and biological molecules.

Xiao M, Wei S, Li Y, Jasensky J, Chen J, Brooks CL 3rd, Chen Z.

Chem Sci. 2017 Nov 30;9(7):1769-1773. doi: 10.1039/c7sc04884j. eCollection 2018 Feb 21.


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

Li Y, Ogorzalek TL, Wei S, Zhang X, Yang P, Jasensky J, Brooks CL, Marsh ENG, Chen Z.

Phys Chem Chem Phys. 2018 Jan 3;20(2):1021-1029. doi: 10.1039/c7cp06063g.


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

Daher M, Mustoe AM, Morriss-Andrews A, Brooks CL III, Walter NG.

Nucleic Acids Res. 2017 Sep 19;45(16):9706-9715. doi: 10.1093/nar/gkx614.


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

Ding X, Hayes RL, Vilseck JZ, Charles MK, Brooks CL 3rd.

J Comput Aided Mol Des. 2018 Jan;32(1):89-102. doi: 10.1007/s10822-017-0050-5. Epub 2017 Sep 7.


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

Kamgar-Parsi K, Hong L, Naito A, Brooks CL 3rd, Ramamoorthy A.

J Biol Chem. 2017 Sep 8;292(36):14963-14976. doi: 10.1074/jbc.M117.791236. Epub 2017 Jul 24.


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

Ding X, Vilseck JZ, Hayes RL, Brooks CL 3rd.

J Chem Theory Comput. 2017 Jun 13;13(6):2501-2510. doi: 10.1021/acs.jctc.7b00204. Epub 2017 May 26.


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

Kim S, Lee J, Jo S, Brooks CL 3rd, Lee HS, Im W.

J Comput Chem. 2017 Jun 5;38(21):1879-1886. doi: 10.1002/jcc.24829. Epub 2017 May 11.


A novel agent SL-401 induces anti-myeloma activity by targeting plasmacytoid dendritic cells, osteoclastogenesis and cancer stem-like cells.

Ray A, Das DS, Song Y, Macri V, Richardson P, Brooks CL, Chauhan D, Anderson KC.

Leukemia. 2017 Dec;31(12):2652-2660. doi: 10.1038/leu.2017.135. Epub 2017 May 8.


Mechanism of Vps4 hexamer function revealed by cryo-EM.

Su M, Guo EZ, Ding X, Li Y, Tarrasch JT, Brooks CL 3rd, Xu Z, Skiniotis G.

Sci Adv. 2017 Apr 14;3(4):e1700325. doi: 10.1126/sciadv.1700325. eCollection 2017 Apr.


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

Wei S, Brooks CL 3rd, Frank AT.

J Comput Chem. 2017 Jun 5;38(15):1270-1274. doi: 10.1002/jcc.24709. Epub 2017 Apr 16.


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

Wei S, Ahlstrom LS, Brooks CL 3rd.

Small. 2017 May;13(18). doi: 10.1002/smll.201603748. Epub 2017 Mar 7.


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

Hayes RL, Armacost KA, Vilseck JZ, Brooks CL 3rd.

J Phys Chem B. 2017 Apr 20;121(15):3626-3635. doi: 10.1021/acs.jpcb.6b09656. Epub 2017 Feb 10.


Glycosylation of MUC1 influences the binding of a therapeutic antibody by altering the conformational equilibrium of the antigen.

Movahedin M, Brooks TM, Supekar NT, Gokanapudi N, Boons GJ, Brooks CL.

Glycobiology. 2017 Jul 1;27(7):677-687. doi: 10.1093/glycob/cww131.


Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).

Won SJ, Davda D, Labby KJ, Hwang SY, Pricer R, Majmudar JD, Armacost KA, Rodriguez LA, Rodriguez CL, Chong FS, Torossian KA, Palakurthi J, Hur ES, Meagher JL, Brooks CL 3rd, Stuckey JA, Martin BR.

ACS Chem Biol. 2016 Dec 16;11(12):3374-3382. Epub 2016 Oct 31.


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

Bruno PA, Morriss-Andrews A, Henderson AR, Brooks CL 3rd, Mapp AK.

Angew Chem Int Ed Engl. 2016 Nov 21;55(48):14997-15001. doi: 10.1002/anie.201607990. Epub 2016 Oct 28.


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

Salmon L, Ahlstrom LS, Horowitz S, Dickson A, Brooks CL 3rd, Bardwell JC.

J Am Chem Soc. 2016 Aug 10;138(31):9826-39. doi: 10.1021/jacs.6b02382. Epub 2016 Aug 2.


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

Arthur EJ, Brooks CL 3rd.

J Comput Chem. 2016 Sep 15;37(24):2171-80. doi: 10.1002/jcc.24435. Epub 2016 Jul 12.


Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions.

Soteras Gutiérrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL 3rd, MacKerell AD Jr.

Bioorg Med Chem. 2016 Oct 15;24(20):4812-4825. doi: 10.1016/j.bmc.2016.06.034. Epub 2016 Jun 18.


Visualizing chaperone-assisted protein folding.

Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL 3rd, Bardwell JC.

Nat Struct Mol Biol. 2016 Jul;23(7):691-7. doi: 10.1038/nsmb.3237. Epub 2016 May 30.


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

Aggarwal A, May ER, Brooks CL 3rd, Klug WS.

Phys Rev E. 2016 Jan;93(1):012417. doi: 10.1103/PhysRevE.93.012417. Epub 2016 Jan 28.


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

Arthur EJ, Brooks CL 3rd.

J Comput Chem. 2016 Apr 15;37(10):927-39. doi: 10.1002/jcc.24280. Epub 2016 Jan 20.



Post CB, Brooks CL 3rd.

Protein Sci. 2016 Jan;25(1):5-8. doi: 10.1002/pro.2851. No abstract available.


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

Gagnon JK, Law SM, Brooks CL 3rd.

J Comput Chem. 2016 Mar 30;37(8):753-62. doi: 10.1002/jcc.24259. Epub 2015 Dec 21.


CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL 3rd, MacKerell AD Jr, Klauda JB, Im W.

J Chem Theory Comput. 2016 Jan 12;12(1):405-13. doi: 10.1021/acs.jctc.5b00935. Epub 2015 Dec 3.


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

Armacost KA, Goh GB, Brooks CL 3rd.

J Chem Theory Comput. 2015 Mar 10;11(3):1267-77. doi: 10.1021/ct500894k.


Single-chain antibody-fragment M6P-1 possesses a mannose 6-phosphate monosaccharide-specific binding pocket that distinguishes N-glycan phosphorylation in a branch-specific manner†.

Blackler RJ, Evans DW, Smith DF, Cummings RD, Brooks CL, Braulke T, Liu X, Evans SV, Müller-Loennies S.

Glycobiology. 2016 Feb;26(2):181-92. doi: 10.1093/glycob/cwv093. Epub 2015 Oct 26.


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

Mustoe AM, Al-Hashimi HM, Brooks CL 3rd.

Nucleic Acids Res. 2016 Jan 8;44(1):402-12. doi: 10.1093/nar/gkv1055. Epub 2015 Oct 19.


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

Wijeyesakere SJ, Gagnon JK, Arora K, Brooks CL 3rd, Raghavan M.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5608-17. doi: 10.1073/pnas.1510132112. Epub 2015 Sep 29.


Directed evolution of the Escherichia coli cAMP receptor protein at the cAMP pocket.

Gunasekara SM, Hicks MN, Park J, Brooks CL, Serate J, Saunders CV, Grover SK, Goto JJ, Lee JW, Youn H.

J Biol Chem. 2015 Oct 30;290(44):26587-96. doi: 10.1074/jbc.M115.678474. Epub 2015 Sep 16.


Protein-Protein Interfaces in Viral Capsids Are Structurally Unique.

Cheng S, Brooks CL 3rd.

J Mol Biol. 2015 Nov 6;427(22):3613-3624. doi: 10.1016/j.jmb.2015.09.008. Epub 2015 Sep 12.


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

Dickson A, Ahlstrom LS, Brooks CL 3rd.

J Comput Chem. 2016 Mar 5;37(6):587-94. doi: 10.1002/jcc.24004. Epub 2015 Aug 6.


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

Ding B, Panahi A, Ho JJ, Laaser JE, Brooks CL 3rd, Zanni MT, Chen Z.

J Am Chem Soc. 2015 Aug 19;137(32):10190-8. doi: 10.1021/jacs.5b04024. Epub 2015 Aug 11.


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

Ogorzalek TL, Wei S, Liu Y, Wang Q, Brooks CL 3rd, Chen Z, Marsh EN.

Langmuir. 2015 Jun 9;31(22):6145-53. doi: 10.1021/acs.langmuir.5b01735. Epub 2015 May 27.


Accurate modeling of ionic surfactants at high concentration.

Goh GB, Eike DM, Murch BP, Brooks CL 3rd.

J Phys Chem B. 2015 May 21;119(20):6217-24. doi: 10.1021/acs.jpcb.5b01765. Epub 2015 May 7.


Membrane environment modulates the pKa values of transmembrane helices.

Panahi A, Brooks CL 3rd.

J Phys Chem B. 2015 Apr 2;119(13):4601-7. doi: 10.1021/acs.jpcb.5b00289. Epub 2015 Mar 22.


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

Mustoe AM, Liu X, Lin PJ, Al-Hashimi HM, Fierke CA, Brooks CL 3rd.

J Am Chem Soc. 2015 Mar 18;137(10):3592-9. doi: 10.1021/ja5130308. Epub 2015 Mar 9.


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

Carrillo-Tripp M, Montiel-García DJ, Brooks CL 3rd, Reddy VS.

J Struct Biol. 2015 Apr;190(1):47-55. doi: 10.1016/j.jsb.2015.02.003. Epub 2015 Feb 16.


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

Laricheva EN, Goh GB, Dickson A, Brooks CL 3rd.

J Am Chem Soc. 2015 Mar 4;137(8):2892-900. doi: 10.1021/ja509233r. Epub 2015 Feb 18.


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

Zeng X, Mukhopadhyay S, Brooks CL 3rd.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2034-9. doi: 10.1073/pnas.1414190112. Epub 2015 Feb 2.


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

Cheng S, Zhang Y, Brooks CL 3rd.

BMC Bioinformatics. 2015 Feb 1;16:33. doi: 10.1186/s12859-015-0471-x.


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

Frank AT, Law SM, Ahlstrom LS, Brooks CL 3rd.

J Chem Theory Comput. 2015 Jan 13;11(1):325-31. doi: 10.1021/ct5009125.


Multiscale modeling of a conditionally disordered pH-sensing chaperone.

Ahlstrom LS, Law SM, Dickson A, Brooks CL 3rd.

J Mol Biol. 2015 Apr 24;427(8):1670-80. doi: 10.1016/j.jmb.2015.01.002. Epub 2015 Jan 10.


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

Yesselman JD, Horowitz S, Brooks CL 3rd, Trievel RC.

Proteins. 2015 Mar;83(3):403-410. doi: 10.1002/prot.24724. Epub 2015 Jan 21.


In situ proteolysis, crystallization and preliminary X-ray diffraction analysis of a VHH that binds listeria internalin B.

Huh I, Gene R, Kumaran J, MacKenzie CR, Brooks CL.

Acta Crystallogr F Struct Biol Commun. 2014 Nov;70(Pt 11):1532-5. doi: 10.1107/S2053230X1402010X. Epub 2014 Oct 25.


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

Dickson A, Mustoe AM, Salmon L, Brooks CL 3rd.

Nucleic Acids Res. 2014 Oct 29;42(19):12126-37. doi: 10.1093/nar/gku799. Epub 2014 Oct 7.


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

Law SM, Ahlstrom LS, Panahi A, Brooks CL 3rd.

J Phys Chem Lett. 2014 Oct 2;5(19):3441-3444. Epub 2014 Sep 19.


The structure of lactoferrin-binding protein B from Neisseria meningitidis suggests roles in iron acquisition and neutralization of host defences.

Brooks CL, Arutyunova E, Lemieux MJ.

Acta Crystallogr F Struct Biol Commun. 2014 Oct;70(Pt 10):1312-7. doi: 10.1107/S2053230X14019372. Epub 2014 Sep 25.

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