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Items: 32

1.

From Inhibition to Degradation: Targeting the Antiapoptotic Protein Myeloid Cell Leukemia 1 (MCL1).

Papatzimas JW, Gorobets E, Maity R, Muniyat MI, MacCallum JL, Neri P, Bahlis NJ, Derksen DJ.

J Med Chem. 2019 Jun 13;62(11):5522-5540. doi: 10.1021/acs.jmedchem.9b00455. Epub 2019 Jun 4.

PMID:
31117518
2.

High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid-State NMR Restraints.

Perez A, Gaalswyk K, Jaroniec CP, MacCallum JL.

Angew Chem Int Ed Engl. 2019 May 13;58(20):6564-6568. doi: 10.1002/anie.201811895. Epub 2019 Apr 17.

PMID:
30913341
3.

Online Optimization of Total Acceptance in Hamiltonian Replica Exchange Simulations.

MacCallum JL, Muniyat MI, Gaalswyk K.

J Phys Chem B. 2018 May 31;122(21):5448-5457. doi: 10.1021/acs.jpcb.7b11778. Epub 2018 Apr 4.

PMID:
29584433
4.

The emerging role of physical modeling in the future of structure determination.

Gaalswyk K, Muniyat MI, MacCallum JL.

Curr Opin Struct Biol. 2018 Apr;49:145-153. doi: 10.1016/j.sbi.2018.03.005. Epub 2018 Mar 16. Review.

PMID:
29554555
5.

Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods.

Pilla KB, Gaalswyk K, MacCallum JL.

Biochim Biophys Acta Proteins Proteom. 2017 Nov;1865(11 Pt B):1654-1663. doi: 10.1016/j.bbapap.2017.06.016. Epub 2017 Jun 22. Review.

PMID:
28648524
6.

Blind protein structure prediction using accelerated free-energy simulations.

Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA.

Sci Adv. 2016 Nov 11;2(11):e1601274. eCollection 2016 Nov.

7.

Constraint methods that accelerate free-energy simulations of biomolecules.

Perez A, MacCallum JL, Coutsias EA, Dill KA.

J Chem Phys. 2015 Dec 28;143(24):243143. doi: 10.1063/1.4936911. Review.

8.

Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.

Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA.

J Chem Theory Comput. 2015 Oct 13;11(10):4770-9. doi: 10.1021/acs.jctc.5b00662. Epub 2015 Sep 17.

9.

Accelerating molecular simulations of proteins using Bayesian inference on weak information.

Perez A, MacCallum JL, Dill KA.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11846-51. doi: 10.1073/pnas.1515561112. Epub 2015 Sep 8.

10.

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.

MacCallum JL, Perez A, Dill KA.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):6985-90. doi: 10.1073/pnas.1506788112. Epub 2015 May 18.

11.

Extracting representative structures from protein conformational ensembles.

Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL.

Proteins. 2014 Oct;82(10):2671-80. doi: 10.1002/prot.24633. Epub 2014 Jul 5.

PMID:
24975328
12.

Single molecule conformational memory extraction: p5ab RNA hairpin.

Pressé S, Peterson J, Lee J, Elms P, MacCallum JL, Marqusee S, Bustamante C, Dill K.

J Phys Chem B. 2014 Jun 19;118(24):6597-603. doi: 10.1021/jp500611f. Epub 2014 Jun 5.

13.

Computing the relative stabilities and the per-residue components in protein conformational changes.

Roy A, Perez A, Dill KA, Maccallum JL.

Structure. 2014 Jan 7;22(1):168-75. doi: 10.1016/j.str.2013.10.015. Epub 2013 Dec 5.

14.

The protein-folding problem, 50 years on.

Dill KA, MacCallum JL.

Science. 2012 Nov 23;338(6110):1042-6. doi: 10.1126/science.1219021. Review.

PMID:
23180855
15.

FlexE: Using elastic network models to compare models of protein structure.

Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL.

J Chem Theory Comput. 2012 Oct 9;8(10):3985-3991.

16.

Assessment of protein structure refinement in CASP9.

MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA.

Proteins. 2011;79 Suppl 10:74-90. doi: 10.1002/prot.23131. Epub 2011 Aug 30.

17.

Hydrophobicity scales: a thermodynamic looking glass into lipid-protein interactions.

MacCallum JL, Tieleman DP.

Trends Biochem Sci. 2011 Dec;36(12):653-62. doi: 10.1016/j.tibs.2011.08.003. Epub 2011 Sep 18. Review.

PMID:
21930386
18.

Transfer of arginine into lipid bilayers is nonadditive.

MacCallum JL, Bennett WF, Tieleman DP.

Biophys J. 2011 Jul 6;101(1):110-7. doi: 10.1016/j.bpj.2011.05.038.

19.

Assessment of the protein-structure refinement category in CASP8.

MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA.

Proteins. 2009;77 Suppl 9:66-80. doi: 10.1002/prot.22538.

20.

Molecular view of cholesterol flip-flop and chemical potential in different membrane environments.

Bennett WF, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP.

J Am Chem Soc. 2009 Sep 9;131(35):12714-20. doi: 10.1021/ja903529f.

PMID:
19673519
21.

Thermodynamic analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes.

Bennett WF, MacCallum JL, Tieleman DP.

J Am Chem Soc. 2009 Feb 11;131(5):1972-8. doi: 10.1021/ja808541r.

PMID:
19146400
22.

Distribution of amino acids in a lipid bilayer from computer simulations.

MacCallum JL, Bennett WF, Tieleman DP.

Biophys J. 2008 May 1;94(9):3393-404. doi: 10.1529/biophysj.107.112805. Epub 2008 Jan 22.

23.

Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment.

MacCallum JL, Bennett WF, Tieleman DP.

J Gen Physiol. 2007 May;129(5):371-7. Epub 2007 Apr 16. No abstract available.

24.

Hydrophobic association of alpha-helices, steric dewetting, and enthalpic barriers to protein folding.

MacCallum JL, Moghaddam MS, Chan HS, Tieleman DP.

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6206-10. Epub 2007 Apr 2. Erratum in: Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19561.

25.

Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins.

Tieleman DP, Maccallum JL, Ash WL, Kandt C, Xu Z, Monticelli L.

J Phys Condens Matter. 2006 Jul 19;18(28):S1221-34. doi: 10.1088/0953-8984/18/28/S07. Epub 2006 Jun 28.

PMID:
21690838
26.
27.

Direct simulation of transmembrane helix association: role of asparagines.

Stockner T, Ash WL, MacCallum JL, Tieleman DP.

Biophys J. 2004 Sep;87(3):1650-6.

28.
29.

Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor.

Monticelli L, Robertson KM, MacCallum JL, Tieleman DP.

FEBS Lett. 2004 Apr 30;564(3):325-32.

30.
31.

Molecular dynamics simulations of pentapeptides at interfaces: salt bridge and cation-pi interactions.

Aliste MP, MacCallum JL, Tieleman DP.

Biochemistry. 2003 Aug 5;42(30):8976-87.

PMID:
12885230
32.

Structures of neat and hydrated 1-octanol from computer simulations.

MacCallum JL, Tieleman DP.

J Am Chem Soc. 2002 Dec 18;124(50):15085-93.

PMID:
12475354

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