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Items: 1 to 20 of 99

1.

NMR-assisted protein structure prediction with MELDxMD.

Robertson JC, Nassar R, Liu C, Brini E, Dill KA, Perez A.

Proteins. 2019 Dec;87(12):1333-1340. doi: 10.1002/prot.25788. Epub 2019 Aug 8.

PMID:
31350773
2.

Protein structure prediction assisted with sparse NMR data in CASP13.

Sala D, Huang YJ, Cole CA, Snyder DA, Liu G, Ishida Y, Swapna GVT, Brock KP, Sander C, Fidelis K, Kryshtafovych A, Inouye M, Tejero R, Valafar H, Rosato A, Montelione GT.

Proteins. 2019 Dec;87(12):1315-1332. doi: 10.1002/prot.25837.

PMID:
31603581
3.

Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13.

Kuenze G, Meiler J.

Proteins. 2019 Dec;87(12):1341-1350. doi: 10.1002/prot.25769. Epub 2019 Jul 18.

PMID:
31292988
4.

Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles.

Chan-Yao-Chong M, Durand D, Ha-Duong T.

J Chem Inf Model. 2019 May 28;59(5):1743-1758. doi: 10.1021/acs.jcim.8b00928. Epub 2019 Mar 18.

PMID:
30840442
5.
6.

Prediction of protein oligomer structures using GALAXY in CASP13.

Baek M, Park T, Woo H, Seok C.

Proteins. 2019 Dec;87(12):1233-1240. doi: 10.1002/prot.25814. Epub 2019 Oct 9.

PMID:
31509276
7.
9.
10.

Comparison of aqueous molecular dynamics with NMR relaxation and residual dipolar couplings favors internal motion in a mannose oligosaccharide.

Almond A, Bunkenborg J, Franch T, Gotfredsen CH, Duus JO.

J Am Chem Soc. 2001 May 23;123(20):4792-802.

PMID:
11457289
11.

A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data.

Zeng J, Roberts KE, Zhou P, Donald BR.

J Comput Biol. 2011 Nov;18(11):1661-79. doi: 10.1089/cmb.2011.0172. Epub 2011 Oct 4.

12.

Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

Zagrovic B, van Gunsteren WF.

Proteins. 2006 Apr 1;63(1):210-8.

PMID:
16425239
13.

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations.

Frank AO, Freudenberger JC, Shaytan AK, Kessler H, Luy B.

Magn Reson Chem. 2015 Mar;53(3):213-7. doi: 10.1002/mrc.4181. Epub 2015 Jan 22.

PMID:
25612077
15.

Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences.

Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE.

Proteins. 2019 Dec;87(12):1298-1314. doi: 10.1002/prot.25827. Epub 2019 Oct 16.

PMID:
31589784
16.
17.

Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain.

Cukier RI.

J Phys Chem B. 2018 Oct 4;122(39):9087-9101. doi: 10.1021/acs.jpcb.8b05797. Epub 2018 Sep 25.

PMID:
30204435
18.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction.

Lehtivarjo J, Tuppurainen K, Hassinen T, Laatikainen R, Peräkylä M.

J Biomol NMR. 2012 Mar;52(3):257-67. doi: 10.1007/s10858-012-9609-6.

PMID:
22314705
19.

Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

Dolenc J, Missimer JH, Steinmetz MO, van Gunsteren WF.

J Biomol NMR. 2010 Jul;47(3):221-35. doi: 10.1007/s10858-010-9425-9. Epub 2010 Jun 4.

PMID:
20524044
20.

MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.

Robertson JC, Perez A, Dill KA.

J Chem Theory Comput. 2018 Dec 11;14(12):6734-6740. doi: 10.1021/acs.jctc.8b00886. Epub 2018 Nov 21.

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