Crossref
journal-article
Springer Science and Business Media LLC
Journal of Biomolecular NMR (297)
References
56
Referenced
77
-
Beauchamp KA, Lin YS, Das R, Pande VS (2012) Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. J Chem Theory Comput 8:1409–1414
(
10.1021/ct2007814
) / J Chem Theory Comput by KA Beauchamp (2012) -
Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS—a message-passing parallel molecular-dynamics implementation. Comput Phys Commun 91:43–56
(
10.1016/0010-4655(95)00042-E
) / Comput Phys Commun by HJC Berendsen (1995) -
Berjanskii MV, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970–14971
(
10.1021/ja054842f
) / J Am Chem Soc by MV Berjanskii (2005) -
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242
(
10.1093/nar/28.1.235
) / Nucleic Acids Res by HM Berman (2000) -
Brüschweiler R, Case DA (1994) Adding harmonic motion to the Karplus relation for spin–spin coupling. J Am Chem Soc 116:11199–11200
(
10.1021/ja00103a062
) / J Am Chem Soc by R Brüschweiler (1994) -
Buck M, Bouguet-Bonnet S, Pastor RW, MacKerell AD (2006) Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J 90:L36–L38
(
10.1529/biophysj.105.078154
) / Biophys J by M Buck (2006) -
Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104:9615–9620
(
10.1073/pnas.0610313104
) / Proc Natl Acad Sci USA by A Cavalli (2007) -
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012
(
10.1002/jcc.10349
) / J Comput Chem by Y Duan (2003) -
Haigh CW, Mallion RB (1972) New tables of ring current shielding in proton magnetic-resonance. Org Magn Res 4:203–228
(
10.1002/mrc.1270040203
) / Org Magn Res by CW Haigh (1972) -
Haigh CW, Mallion RB (1979) Ring current theories in nuclear magnetic-resonance. Prog NMR Spectrosc 13:303–344
(
10.1016/0079-6565(79)80010-2
) / Prog NMR Spectrosc by CW Haigh (1979) -
Han B, Liu YF, Ginzinger SW, Wishart DS (2011) SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR 50:43–57
(
10.1007/s10858-011-9478-4
) / J Biomol NMR by B Han (2011) -
Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
(
10.1021/ct700301q
) / J Chem Theory Comput by B Hess (2008) -
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65:712–725
(
10.1002/prot.21123
) / Proteins by V Hornak (2006) -
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential function for simulating liquid water. J Chem Phys 79:926–935
(
10.1063/1.445869
) / J Chem Phys by WL Jorgensen (1983) -
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 19:120–127
(
10.1016/j.sbi.2009.03.004
) / Curr Opin Struct Biol by JL Klepeis (2009) -
Kohlhoff KJ, Robustelli P, Cavalli A, Salvatella X, Vendruscolo M (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131:13894–13895
(
10.1021/ja903772t
) / J Am Chem Soc by KJ Kohlhoff (2009) -
Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE (2010) A transient and low-populated protein-folding intermediate at atomic resolution. Science 329:1312–1316
(
10.1126/science.1191723
) / Science by DM Korzhnev (2010) -
Lange OF, van der Spoel D, de Groot BL (2010) Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J 99:647–655
(
10.1016/j.bpj.2010.04.062
) / Biophys J by OF Lange (2010) -
Lehtivarjo J, Hassinen T, Korhonen SP, Perakyla M, Laatikainen R (2009) 4D prediction of protein H-1 chemical shifts. J Biomol NMR 45:413–426
(
10.1007/s10858-009-9384-1
) / J Biomol NMR by J Lehtivarjo (2009) -
Lehtivarjo J, Tuppurainen K, Hassinen T, Laatikainen R, Perakyla M (2012) Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction. J Biomol NMR 52:257–267
(
10.1007/s10858-012-9609-6
) / J Biomol NMR by J Lehtivarjo (2012) -
Li DW, Brüschweiler R (2010a) NMR-based protein potentials. Angew Chem 49:6778–6780
(
10.1002/anie.201001898
) / Angew Chem by DW Li (2010) -
Li DW, Brüschweiler R (2010b) Certification of molecular dynamics trajectories with NMR chemical shifts. J Phys Chem Lett 1:246–248
(
10.1021/jz9001345
) / J Phys Chem Lett by DW Li (2010) -
Li DW, Brüschweiler R (2011) Iterative optimization of molecular mechanics force fields from NMR data of full-length proteins. J Chem Theory Comput 7:1773–1782
(
10.1021/ct200094b
) / J Chem Theory Comput by DW Li (2011) -
Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317
(
10.1007/s008940100045
) / J Mol Model by E Lindahl (2001) -
Lindorff-Larsen K, Best RB, Vendruscolo M (2005) Interpreting dynamically-averaged scalar couplings in proteins. J Biomol NMR 32:273–280
(
10.1007/s10858-005-8873-0
) / J Biomol NMR by K Lindorff-Larsen (2005) -
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78:1950–1958
(
10.1002/prot.22711
) / Proteins by K Lindorff-Larsen (2010) -
Long D, Li DW, Walter KFA, Griesinger C, Brüschweiler R (2011) Toward a predictive understanding of slow methyl group dynamics in proteins. Biophys J 101:910–915
(
10.1016/j.bpj.2011.06.053
) / Biophys J by D Long (2011) -
Markwick PRL, Bouvignies G, Blackledge M (2007) Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J Am Chem Soc 129:4724–4730
(
10.1021/ja0687668
) / J Am Chem Soc by PRL Markwick (2007) -
Markwick PR, Showalter SA, Bouvignies G, Brüschweiler R, Blackledge M (2009) Structural dynamics of protein backbone phi angles: extended molecular dynamics simulations versus experimental (3) J scalar couplings. J Biomol NMR 45:17–21
(
10.1007/s10858-009-9341-z
) / J Biomol NMR by PR Markwick (2009) -
Markwick PRL, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA (2010) Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc 132:1220–1221
(
10.1021/ja9093692
) / J Am Chem Soc by PRL Markwick (2010) -
McConnell HM (1957) Theory of nuclear magnetic shielding in molecules. I. Long-range dipolar shielding of protons. J Chem Phys 27:226–229
(
10.1063/1.1743676
) / J Chem Phys by HM McConnell (1957) -
Meiler J, Prompers JJ, Peti W, Griesinger C, Brüschweiler R (2001) Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J Am Chem Soc 123:6098–6107
(
10.1021/ja010002z
) / J Am Chem Soc by J Meiler (2001) -
Moon S, Case DA (2007) A new model for chemical shifts of amide hydrogens in proteins. J Biomol NMR 38:139–150
(
10.1007/s10858-007-9156-8
) / J Biomol NMR by S Moon (2007) -
Neal S, Nip AM, Zhang HY, Wishart DS (2003) Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts. J Biomol NMR 26:215–240
(
10.1023/A:1023812930288
) / J Biomol NMR by S Neal (2003) -
Osapay K, Case DA (1991) A new analysis of proton chemical-shifts in proteins. J Am Chem Soc 113:9436–9444
(
10.1021/ja00025a002
) / J Am Chem Soc by K Osapay (1991) -
Robustelli P, Stafford KA, Palmer AG (2012) Interpreting protein structural dynamics from NMR chemical shifts. J Am Chem Soc 134:6365–6374
(
10.1021/ja300265w
) / J Am Chem Soc by P Robustelli (2012) -
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Guntert P, He YF, Herrmann T, Huang YPJ, Jaravine V, Jonker HRA, Kennedy MA, Lange OF, Liu GH, Malliavin TE, Mani R, Mao BC, Montelione GT, Nilges M, Rossi P, van dS, G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, de V, S, Vuister GW, Wu B, Yang YH, Bonvin AMJJ (2012) Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20:227–236
(
10.1016/j.str.2012.01.002
) -
Ruschak AM, Religa TL, Breuer S, Witt S, Kay LE (2010) The proteasome antechamber maintains substrates in an unfolded state. Nature 467:868–871
(
10.1038/nature09444
) / Nature by AM Ruschak (2010) -
Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M (2011) Structure-based prediction of methyl chemical shifts in proteins. J Biomol NMR 50:331–346
(
10.1007/s10858-011-9524-2
) / J Biomol NMR by AB Sahakyan (2011) -
Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289–302
(
10.1007/s10858-007-9166-6
) / J Biomol NMR by Y Shen (2007) -
Shen Y, Bax A (2010) SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48:13–22
(
10.1007/s10858-010-9433-9
) / J Biomol NMR by Y Shen (2010) -
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685–4690
(
10.1073/pnas.0800256105
) / Proc Natl Acad Sci USA by Y Shen (2008) -
Shen Y, Vernon R, Baker D, Bax A (2009) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43:63–78
(
10.1007/s10858-008-9288-5
) / J Biomol NMR by Y Shen (2009) -
Showalter SA, Brüschweiler R (2007) Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: application to the AMBER99SB force field. J Chem Theory Comput 3:961–975
(
10.1021/ct7000045
) / J Chem Theory Comput by SA Showalter (2007) -
Showalter SA, Johnson E, Rance M, Brüschweiler R (2007) Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. J Am Chem Soc 129:14146–14147
(
10.1021/ja075976r
) / J Am Chem Soc by SA Showalter (2007) -
Trbovic N, Kim B, Friesner RA, Palmer AG (2008) Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation. Proteins 71:684–694
(
10.1002/prot.21750
) / Proteins by N Trbovic (2008) -
Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408
(
10.1093/nar/gkm957
) / Nucleic Acids Res by EL Ulrich (2008) -
Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718
(
10.1002/jcc.20291
) / J Comput Chem by D Spoel Van der (2005) -
Vila JA, Arnautova YA, Martin OA, Scheraga HA (2009) Quantum-mechanics-derived C-13(alpha) chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci USA 106:16972–16977
(
10.1073/pnas.0908833106
) / Proc Natl Acad Sci USA by JA Vila (2009) -
Vogeli B, Ying JF, Grishaev A, Bax A (2007) Limits on variations in protein backbone dynamics from precise measurements of scalar couplings. J Am Chem Soc 129:9377–9385
(
10.1021/ja070324o
) / J Am Chem Soc by B Vogeli (2007) -
Wickstrom L, Okur A, Simmerling C (2009) Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophys J 97:853–856
(
10.1016/j.bpj.2009.04.063
) / Biophys J by L Wickstrom (2009) -
Xu XP, Case DA (2001) Automated prediction of 15N, 13Calpha, 13Cbeta and 13C′ chemical shifts in proteins using a density functional database. J Biomol NMR 21:321–333
(
10.1023/A:1013324104681
) / J Biomol NMR by XP Xu (2001) -
Xu XP, Case DA (2002) Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65:408–423
(
10.1002/bip.10276
) / Biopolymers by XP Xu (2002) -
Xue Y, Ward JM, Yuwen TR, Podkorytov IS, Skrynnikov NR (2012) Microsecond time-scale conformational exchange in proteins: using long molecular dynamics trajectory to simulate NMR relaxation dispersion data. J Am Chem Soc 134:2555–2562
(
10.1021/ja206442c
) / J Am Chem Soc by Y Xue (2012) -
Zhang F, Brüschweiler R (2002) Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc 124:12654–12655
(
10.1021/ja027847a
) / J Am Chem Soc by F Zhang (2002) -
Zhang H, Neal S, Wishart DS (2003) RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR 25:173–195
(
10.1023/A:1022836027055
) / J Biomol NMR by H Zhang (2003)
Dates
Type | When |
---|---|
Created | 12 years, 11 months ago (Sept. 12, 2012, 6:33 a.m.) |
Deposited | 3 years, 7 months ago (Jan. 28, 2022, 2:34 p.m.) |
Indexed | 1 week, 3 days ago (Aug. 21, 2025, 1:35 p.m.) |
Issued | 12 years, 11 months ago (Sept. 13, 2012) |
Published | 12 years, 11 months ago (Sept. 13, 2012) |
Published Online | 12 years, 11 months ago (Sept. 13, 2012) |
Published Print | 12 years, 10 months ago (Nov. 1, 2012) |
@article{Li_2012, title={PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles}, volume={54}, ISSN={1573-5001}, url={http://dx.doi.org/10.1007/s10858-012-9668-8}, DOI={10.1007/s10858-012-9668-8}, number={3}, journal={Journal of Biomolecular NMR}, publisher={Springer Science and Business Media LLC}, author={Li, Da-Wei and Brüschweiler, Rafael}, year={2012}, month=sep, pages={257–265} }