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Items: 1 to 50 of 354

1.

A double exponential potential for van der Waals interaction.

Wu X, Brooks BR.

AIP Adv. 2019 Jun 7;9(6):065304. doi: 10.1063/1.5107505. eCollection 2019 Jun.

3.

An Albumin Sandwich Enhances in Vivo Circulation and Stability of Metabolically Labile Peptides.

Tian R, Zhu S, Zeng Q, Lang L, Ma Y, Kiesewetter DO, Liu Y, Fu X, Lau J, Zhu G, Jacobson O, Wang Z, Dai Y, Yu G, Brooks BR, Liu G, Niu G, Chen X.

Bioconjug Chem. 2019 Jun 19;30(6):1711-1723. doi: 10.1021/acs.bioconjchem.9b00258. Epub 2019 Jun 6.

PMID:
31082207
4.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

Krämer A, Pickard FC 4th, Huang J, Venable RM, Simmonett AC, Reith D, Kirschner KN, Pastor RW, Brooks BR.

J Chem Theory Comput. 2019 Jun 11;15(6):3854-3867. doi: 10.1021/acs.jctc.9b00016. Epub 2019 May 9.

5.

Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials.

van den Berg LH, Sorenson E, Gronseth G, Macklin EA, Andrews J, Baloh RH, Benatar M, Berry JD, Chio A, Corcia P, Genge A, Gubitz AK, Lomen-Hoerth C, McDermott CJ, Pioro EP, Rosenfeld J, Silani V, Turner MR, Weber M, Brooks BR, Miller RG, Mitsumoto H; Airlie House ALS Clinical Trials Guidelines Group.

Neurology. 2019 Apr 2;92(14):e1610-e1623. doi: 10.1212/WNL.0000000000007242. Epub 2019 Mar 8.

6.

Provisional best practices guidelines for the evaluation of bulbar dysfunction in amyotrophic lateral sclerosis.

Pattee GL, Plowman EK, Focht Garand KL, Costello J, Brooks BR, Berry JD, Smith RA, Atassi N, Chapin JL, Yunusova Y, McIlduff CE, Young E, Macklin EA, Locatelli ER, Silani V, Heitzman D, Wymer J, Goutman SA, Gelinas DF, Perry B, Nalipinski P, Stipancic K, O'Brien M, Sullivan SL, Pioro EP, Gargiulo G, Green JR; Contributing Members of the NEALS Bulbar Subcommittee.

Muscle Nerve. 2019 May;59(5):531-536. doi: 10.1002/mus.26408. Epub 2019 Jan 22.

PMID:
30620104
7.

On the convergence of multi-scale free energy simulations.

König G, Brooks BR, Thiel W, York DM.

Mol Simul. 2018;44(13-14):1062-1081. doi: 10.1080/08927022.2018.1475741. Epub 2018 May 30.

8.

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM.

Molecules. 2018 Oct 19;23(10). pii: E2695. doi: 10.3390/molecules23102695.

9.

Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments.

Tywoniuk B, Yuan Y, McCartan S, Szydłowska BM, Tofoleanu F, Brooks BR, Buchete NV.

J Phys Chem B. 2018 Dec 13;122(49):11535-11545. doi: 10.1021/acs.jpcb.8b07423. Epub 2018 Nov 29.

10.

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.

Nishikawa N, Han K, Wu X, Tofoleanu F, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):1075-1086. doi: 10.1007/s10822-018-0166-2. Epub 2018 Oct 15.

11.

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.

Prasad S, Huang J, Zeng Q, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):1191-1201. doi: 10.1007/s10822-018-0167-1. Epub 2018 Oct 1.

PMID:
30276503
12.

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.

Hudson PS, Han K, Woodcock HL, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):983-999. doi: 10.1007/s10822-018-0165-3. Epub 2018 Oct 1.

PMID:
30276502
13.

Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides.

Narayan B, Herbert C, Yuan Y, Rodriguez BJ, Brooks BR, Buchete NV.

J Chem Phys. 2018 Aug 21;149(7):072323. doi: 10.1063/1.5027580.

PMID:
30134732
14.

Reservoir pH replica exchange.

Damjanovic A, Miller BT, Okur A, Brooks BR.

J Chem Phys. 2018 Aug 21;149(7):072321. doi: 10.1063/1.5027413.

PMID:
30134701
15.

Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge.

Zeng Q, Jones MR, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):1179-1189. doi: 10.1007/s10822-018-0150-x. Epub 2018 Aug 20.

PMID:
30128926
16.

Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method.

Han K, Hudson PS, Jones MR, Nishikawa N, Tofoleanu F, Brooks BR.

J Comput Aided Mol Des. 2018 Oct;32(10):1059-1073. doi: 10.1007/s10822-018-0144-8. Epub 2018 Aug 6.

PMID:
30084077
17.

Stage of prolonged survival in ALS.

Brooks BR, Bravver EK, Langford VL, Bockenek WL, Lindblom SS.

Lancet Neurol. 2018 Jul;17(7):579. doi: 10.1016/S1474-4422(18)30207-2. No abstract available.

PMID:
29914701
18.

Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins.

Wu X, Brooks BR.

J Phys Chem B. 2018 Jun 14;122(23):6215-6223. doi: 10.1021/acs.jpcb.8b04584. Epub 2018 Jun 1.

19.

Edaravone in the treatment of amyotrophic lateral sclerosis: efficacy and access to therapy - a roundtable discussion.

Brooks BR, Jorgenson JA, Newhouse BJ, Shefner JM, Agnese W.

Am J Manag Care. 2018 Apr;24(9 Suppl):S175-S186.

20.

Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations.

Tofoleanu F, Yuan Y, Pickard FC 4th, Tywoniuk B, Brooks BR, Buchete NV.

J Phys Chem B. 2018 May 31;122(21):5657-5665. doi: 10.1021/acs.jpcb.7b12083. Epub 2018 Feb 21.

21.

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Leonard AN, Simmonett AC, Pickard FC 4th, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW.

J Chem Theory Comput. 2018 Feb 13;14(2):948-958. doi: 10.1021/acs.jctc.7b00948. Epub 2018 Jan 9.

22.

Best practices protocol for the evaluation of bulbar dysfunction: summary recommendations from the NEALS bulbar subcommittee symposium.

Pattee GL, Plowman EK, Brooks BR, Berry JD, Atassi N, Chapin JL, Garand K, Yunusova Y, Mcilduff CE, Young E, Costello JM, Macklin EA, Locatelli ER, Silani V, Heitzman D, Wymer J, Goutman SA, Gelinas DF, Smith R, Perry B, Nalipinski P, Stipancic K, O'Brien M, Sullivan SL, Green J; CONTRIBUTING MEMBERS OF THE NEALS BULBAR SUBCOMMITTEE.

Amyotroph Lateral Scler Frontotemporal Degener. 2018 May;19(3-4):311-312. doi: 10.1080/21678421.2017.1404109. Epub 2017 Dec 5.

PMID:
29205054
23.

A randomized controlled trial of resistance and endurance exercise in amyotrophic lateral sclerosis.

Clawson LL, Cudkowicz M, Krivickas L, Brooks BR, Sanjak M, Allred P, Atassi N, Swartz A, Steinhorn G, Uchil A, Riley KM, Yu H, Schoenfeld DA, Maragakis NJ; neals consortium.

Amyotroph Lateral Scler Frontotemporal Degener. 2018 May;19(3-4):250-258. doi: 10.1080/21678421.2017.1404108. Epub 2017 Nov 30.

PMID:
29191052
24.

Implementation of a Regional Training Program on African Swine Fever As Part of the Cooperative Biological Engagement Program across the Caucasus Region.

De Nardi M, Léger A, Stepanyan T, Khachatryan B, Karibayev T, Sytnik I, Tyulegenov S, Akhmetova A, Nychyk S, Sytiuk M, Nevolko O, Datsenko R, Chaligava T, Avaliani L, Parkadze O, Ninidze L, Kartskhia N, Napetvaridze T, Asanishvili Z, Khelaia D, Menteshashvili I, Zadayan M, Niazyan L, Mykhaylovska N, Brooks BR, Zhumabayeva G, Satabayeva S, Metreveli M, Gallagher T, Obiso R.

Front Vet Sci. 2017 Oct 26;4:164. doi: 10.3389/fvets.2017.00164. eCollection 2017.

25.

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Huang J, Simmonett AC, Pickard FC 4th, MacKerell AD Jr, Brooks BR.

J Chem Phys. 2017 Oct 28;147(16):161702. doi: 10.1063/1.4984113.

26.

Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise.

Lee J, Zhang ZY, Lee J, Brooks BR, Ahn YY.

Sci Rep. 2017 Sep 29;7(1):12399. doi: 10.1038/s41598-017-12432-1.

27.

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

Wang M, Li P, Jia X, Liu W, Shao Y, Hu W, Zheng J, Brooks BR, Mei Y.

J Chem Inf Model. 2017 Oct 23;57(10):2476-2489. doi: 10.1021/acs.jcim.7b00001. Epub 2017 Oct 2.

PMID:
28933850
28.

Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins.

Lee J, Konc J, Janežič D, Brooks BR.

Sci Rep. 2017 Sep 14;7(1):11652. doi: 10.1038/s41598-017-10412-z.

29.

Machine Learning Force Field Parameters from Ab Initio Data.

Li Y, Li H, Pickard FC 4th, Narayanan B, Sen FG, Chan MKY, Sankaranarayanan SKRS, Brooks BR, Roux B.

J Chem Theory Comput. 2017 Sep 12;13(9):4492-4503. doi: 10.1021/acs.jctc.7b00521. Epub 2017 Sep 1.

30.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS.

PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul.

31.

Finding multiple reaction pathways via global optimization of action.

Lee J, Lee IH, Joung I, Lee J, Brooks BR.

Nat Commun. 2017 May 26;8:15443. doi: 10.1038/ncomms15443.

32.

Six-Minute Walk Test as a Measure of Walking Capacity in Ambulatory Individuals With Amyotrophic Lateral Sclerosis.

Sanjak M, Langford V, Holsten S, Rozario N, Patterson CGM, Bravver E, Bockenek WL, Brooks BR.

Arch Phys Med Rehabil. 2017 Nov;98(11):2301-2307. doi: 10.1016/j.apmr.2017.04.004. Epub 2017 Apr 30.

PMID:
28465220
33.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Huang J, Mei Y, König G, Simmonett AC, Pickard FC 4th, Wu Q, Wang LP, MacKerell AD Jr, Brooks BR, Shao Y.

J Chem Theory Comput. 2017 Feb 14;13(2):679-695. doi: 10.1021/acs.jctc.6b01125. Epub 2017 Jan 24.

34.

Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

Wu X, Lee J, Brooks BR.

J Phys Chem B. 2017 Apr 20;121(15):3318-3330. doi: 10.1021/acs.jpcb.6b08249. Epub 2016 Oct 18.

35.

An empirical extrapolation scheme for efficient treatment of induced dipoles.

Simmonett AC, Pickard FC 4th, Ponder JW, Brooks BR.

J Chem Phys. 2016 Oct 28;145(16):164101.

36.
37.

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases.

Nagy GN, Suardíaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Tóth J, Vértessy BG, Rosta E.

J Am Chem Soc. 2016 Nov 16;138(45):15035-15045. Epub 2016 Nov 4.

38.

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR.

J Comput Aided Mol Des. 2017 Jan;31(1):107-118. doi: 10.1007/s10822-016-9965-5. Epub 2016 Sep 30.

39.

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Lee J, Tofoleanu F, Pickard FC 4th, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR.

J Comput Aided Mol Des. 2017 Jan;31(1):71-85. doi: 10.1007/s10822-016-9968-2. Epub 2016 Sep 27.

40.

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Pickard FC 4th, König G, Simmonett AC, Shao Y, Brooks BR.

Bioorg Med Chem. 2016 Oct 15;24(20):4988-4997. doi: 10.1016/j.bmc.2016.08.031. Epub 2016 Aug 22.

41.

Partition coefficients for the SAMPL5 challenge using transfer free energies.

Jones MR, Brooks BR, Wilson AK.

J Comput Aided Mol Des. 2016 Nov;30(11):1129-1138. doi: 10.1007/s10822-016-9964-6. Epub 2016 Sep 19.

42.

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections.

Pickard FC 4th, König G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR.

J Comput Aided Mol Des. 2016 Nov;30(11):1087-1100. doi: 10.1007/s10822-016-9955-7. Epub 2016 Sep 19.

PMID:
27646286
43.

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

König G, Pickard FC 4th, Huang J, Simmonett AC, Tofoleanu F, Lee J, Dral PO, Prasad S, Jones M, Shao Y, Thiel W, Brooks BR.

J Comput Aided Mol Des. 2016 Nov;30(11):989-1006. doi: 10.1007/s10822-016-9936-x. Epub 2016 Aug 30.

PMID:
27577746
44.

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

Dybeck EC, König G, Brooks BR, Shirts MR.

J Chem Theory Comput. 2016 Apr 12;12(4):1466-80. doi: 10.1021/acs.jctc.5b01188. Epub 2016 Mar 23.

45.

The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes.

Rinschen MM, Bharill P, Wu X, Kohli P, Reinert MJ, Kretz O, Saez I, Schermer B, Höhne M, Bartram MP, Aravamudhan S, Brooks BR, Vilchez D, Huber TB, Müller RU, Krüger M, Benzing T.

Hum Mol Genet. 2016 Apr 1;25(7):1328-44. doi: 10.1093/hmg/ddw016. Epub 2016 Jan 19.

46.

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

Jia X, Wang M, Shao Y, König G, Brooks BR, Zhang JZ, Mei Y.

J Chem Theory Comput. 2016 Feb 9;12(2):499-511. doi: 10.1021/acs.jctc.5b00920. Epub 2016 Jan 12.

PMID:
26731197
47.

Power Wheelchair Use in Persons With Amyotrophic Lateral Sclerosis: Changes Over Time.

Ward AL, Hammond S, Holsten S, Bravver E, Brooks BR.

Assist Technol. 2015 Winter;27(4):238-45. doi: 10.1080/10400435.2015.1040896.

PMID:
26691564
48.

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

König G, Mei Y, Pickard FC 4th, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y.

J Chem Theory Comput. 2016 Jan 12;12(1):332-44. doi: 10.1021/acs.jctc.5b00874. Epub 2015 Dec 11.

49.

The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential.

Lee J, Joo K, Brooks BR, Lee J.

J Chem Theory Comput. 2015 Jul 14;11(7):3211-24. doi: 10.1021/acs.jctc.5b00268. Epub 2015 Jun 24. Erratum in: J Chem Theory Comput. 2015 Jul 14;11(7):3224.

PMID:
26575758
50.

Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method.

Lee J, Miller BT, Damjanović A, Brooks BR.

J Chem Theory Comput. 2015 Jun 9;11(6):2560-74. doi: 10.1021/ct501101f. Epub 2015 May 26.

PMID:
26575555

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