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Items: 1 to 50 of 423

1.

Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription.

Wang Y, Brooks CL.

J Phys Chem Lett. 2019 Sep 19. doi: 10.1021/acs.jpclett.9b02226. [Epub ahead of print]

PMID:
31535860
2.

Hydroxyl Radical-Coupled Electron-Transfer Mechanism of Flavin-Dependent Hydroxylases.

Tweedy SE, Rodríguez Benítez A, Narayan ARH, Zimmerman PM, Brooks CL 3rd, Wymore T.

J Phys Chem B. 2019 Sep 18. doi: 10.1021/acs.jpcb.9b08178. [Epub ahead of print]

PMID:
31532200
3.

Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods.

Deng H, Ke S, Callender R, Balakrishnan G, Spiro TG, May ER, Brooks CL 3rd.

J Phys Chem B. 2019 Sep 19;123(37):7840-7851. doi: 10.1021/acs.jpcb.9b06759. Epub 2019 Sep 4.

4.

DNA methyltransferase inhibition overcomes diphthamide pathway deficiencies underlying CD123-targeted treatment resistance.

Togami K, Pastika T, Stephansky J, Ghandi M, Christie AL, Jones KL, Johnson CA, Lindsay RW, Brooks CL, Letai A, Craig JW, Pozdnyakova O, Weinstock DM, Montero J, Aster JC, Johannessen CM, Lane AA.

J Clin Invest. 2019 Aug 22. pii: 128571. doi: 10.1172/JCI128571. [Epub ahead of print]

5.

Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.

Vilseck JZ, Sohail N, Hayes RL, Brooks CL 3rd.

J Phys Chem Lett. 2019 Aug 13:4875-4880. doi: 10.1021/acs.jpclett.9b02004. [Epub ahead of print]

PMID:
31386370
6.

Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization.

Benítez AR, Tweedy S, Baker Dockrey SA, Lukowski AL, Wymore T, Khare D, Brooks CL 3rd, Palfey BA, Smith JL, Narayan ARH.

ACS Catal. 2019 Apr 5;9(4):3633-3640. doi: 10.1021/acscatal.8b04575. Epub 2019 Mar 25.

PMID:
31346489
7.

Frustration and folding of a TIM barrel protein.

Halloran KT, Wang Y, Arora K, Chakravarthy S, Irving TC, Bilsel O, Brooks CL 3rd, Matthews CR.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16378-16383. doi: 10.1073/pnas.1900880116. Epub 2019 Jul 25.

PMID:
31346089
8.

Positioning-Group-Enabled Biocatalytic Oxidative Dearomatization.

Dockrey SAB, Suh CE, Benítez AR, Wymore T, Brooks CL 3rd, Narayan ARH.

ACS Cent Sci. 2019 Jun 26;5(6):1010-1016. doi: 10.1021/acscentsci.9b00163. Epub 2019 Jun 12.

9.

Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.

Artikis E, Brooks CL 3rd.

Biophys J. 2019 Jul 23;117(2):258-268. doi: 10.1016/j.bpj.2019.06.003. Epub 2019 Jun 12.

PMID:
31255294
10.

Tagraxofusp in Blastic Plasmacytoid Dendritic-Cell Neoplasm.

Pemmaraju N, Lane AA, Sweet KL, Stein AS, Vasu S, Blum W, Rizzieri DA, Wang ES, Duvic M, Sloan JM, Spence S, Shemesh S, Brooks CL, Balser J, Bergstein I, Lancet JE, Kantarjian HM, Konopleva M.

N Engl J Med. 2019 Apr 25;380(17):1628-1637. doi: 10.1056/NEJMoa1815105.

PMID:
31018069
11.

Structure of a VHH isolated from a naïve phage display library.

White B, Huh I, Brooks CL.

BMC Res Notes. 2019 Mar 19;12(1):154. doi: 10.1186/s13104-019-4197-0.

12.

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.

Ding X, Vilseck JZ, Brooks CL 3rd.

J Chem Theory Comput. 2019 Feb 12;15(2):799-802. doi: 10.1021/acs.jctc.8b01010. Epub 2019 Feb 4.

PMID:
30689377
13.

Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude.

Haji-Ghassemi O, Müller-Loennies S, Brooks CL, MacKenzie CR, Caveney N, Van Petegem F, Brade L, Kosma P, Brade H, Evans SV.

Biochemistry. 2019 Feb 12;58(6):714-726. doi: 10.1021/acs.biochem.8b00318. Epub 2019 Jan 10.

PMID:
30571096
14.

Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity.

Zou X, Wei S, Badieyan S, Schroeder M, Jasensky J, Brooks CL 3rd, Marsh ENG, Chen Z.

J Am Chem Soc. 2018 Dec 5;140(48):16560-16569. doi: 10.1021/jacs.8b08138. Epub 2018 Nov 19.

PMID:
30403342
15.

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.

Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL 3rd, Artsimovitch I, Walter NG.

Mol Cell. 2018 Nov 1;72(3):541-552.e6. doi: 10.1016/j.molcel.2018.08.046.

PMID:
30388413
16.

Immunological Functions and Evolutionary Emergence of Heavy-Chain Antibodies.

Brooks CL, Rossotti MA, Henry KA.

Trends Immunol. 2018 Dec;39(12):956-960. doi: 10.1016/j.it.2018.09.008. Epub 2018 Oct 10. Review.

PMID:
30314850
17.

Reply to 'Misreading chaperone-substrate complexes from random noise'.

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 JCA.

Nat Struct Mol Biol. 2018 Nov;25(11):990-991. doi: 10.1038/s41594-018-0145-2. No abstract available.

PMID:
30297780
18.

VIPERdb: A Tool for Virus Research.

Ho PT, Montiel-Garcia DJ, Wong JJ, Carrillo-Tripp M, Brooks CL 3rd, Johnson JE, Reddy VS.

Annu Rev Virol. 2018 Sep 29;5(1):477-488. doi: 10.1146/annurev-virology-092917-043405.

PMID:
30265627
19.

Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme.

Hayes RL, Vilseck JZ, Brooks CL 3rd.

Protein Sci. 2018 Nov;27(11):1910-1922. doi: 10.1002/pro.3500.

PMID:
30175503
20.

Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators.

Henderson AR, Henley MJ, Foster NJ, Peiffer AL, Beyersdorf MS, Stanford KD, Sturlis SM, Linhares BM, Hill ZB, Wells JA, Cierpicki T, Brooks CL 3rd, Fierke CA, Mapp AK.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):8960-8965. doi: 10.1073/pnas.1806202115. Epub 2018 Aug 20.

21.

"I think that's all a lie…I think It's genocide": Applying a Critical Race Praxis to Youth Perceptions of Flint Water Contamination.

Muhammad M, De Loney EH, Brooks CL, Assari S, Robinson D, Caldwell CH.

Ethn Dis. 2018 Aug 9;28(Suppl 1):241-246. doi: 10.18865/ed.28.S1.241. eCollection 2018.

22.

Structural basis of VHH-mediated neutralization of the food-borne pathogen Listeria monocytogenes.

King MT, Huh I, Shenai A, Brooks TM, Brooks CL.

J Biol Chem. 2018 Aug 31;293(35):13626-13635. doi: 10.1074/jbc.RA118.003888. Epub 2018 Jul 5.

23.

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.

24.

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.

25.

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.

26.

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.

PMID:
29235592
27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

PMID:
26871111
45.

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.

46.

Editorial.

Post CB, Brooks CL 3rd.

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

47.

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.

48.

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.

49.

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.

50.

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.

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