-
1
-
-
1842532008
-
A hierarchical approach to all-atom loop prediction
-
Jacobson MP, Pincus DL, Rapp CS, Day T, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom loop prediction. Proteins 2004;55:351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
2
-
-
0038300292
-
Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects
-
Das B, Meirovitch H. Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects. Proteins 2003;51:470-483.
-
(2003)
Proteins
, vol.51
, pp. 470-483
-
-
Das, B.1
Meirovitch, H.2
-
3
-
-
1042279566
-
Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins
-
Heuser P, Wohlfahrt G, Schomburg D. Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins. Proteins 2004;54:583-595.
-
(2004)
Proteins
, vol.54
, pp. 583-595
-
-
Heuser, P.1
Wohlfahrt, G.2
Schomburg, D.3
-
4
-
-
1642575364
-
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
-
Zhang C, Song L, Zhou Y. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Prot Sci 2004;13:391-399.
-
(2004)
Prot Sci
, vol.13
, pp. 391-399
-
-
Zhang, C.1
Song, L.2
Zhou, Y.3
-
5
-
-
20444490870
-
Determining protein topology from skeletons of secondary structures
-
Wu Y, Chen M, Lu M, Wang Q, Ma J. Determining protein topology from skeletons of secondary structures. J Mol Biol 2005;350:571-586.
-
(2005)
J Mol Biol
, vol.350
, pp. 571-586
-
-
Wu, Y.1
Chen, M.2
Lu, M.3
Wang, Q.4
Ma, J.5
-
6
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
Misura KMS, Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins 2005;59:15-29.
-
(2005)
Proteins
, vol.59
, pp. 15-29
-
-
Misura, K.M.S.1
Baker, D.2
-
7
-
-
24644439203
-
Prediction of the conformation and geometry of loops in globular proteins: Testing Arch DB, a structural classification of loops
-
Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg M, Oliba B. Prediction of the conformation and geometry of loops in globular proteins: Testing Arch DB, a structural classification of loops. Proteins 2005;60:746-757.
-
(2005)
Proteins
, vol.60
, pp. 746-757
-
-
Fernandez-Fuentes, N.1
Querol, E.2
Aviles, F.X.3
Sternberg, M.4
Oliba, B.5
-
8
-
-
0033954256
-
The Protein Databank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Databank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
9
-
-
21044449889
-
RECOORD: A RE-calculated COORdinates database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Guntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJ. RECOORD: a RE-calculated COORdinates database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 2004;59:662-672.
-
(2004)
Proteins
, vol.59
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
Miller, Z.4
Spronk, C.A.E.M.5
Nabuurs, S.B.6
Guntert, P.7
Livny, M.8
Markley, J.L.9
Nilges, M.10
Ulrich, E.L.11
Kaptein, R.12
Bonvin, A.M.J.J.13
-
10
-
-
28444480251
-
Comparison of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination
-
Snyder DA, Chen Y, Denissova NG, Acton T, Aramini JM, Ciano M, Karlin R, Liu J, Manor P, Rajan PA, Rossi P, Swapna GVT, Xiao R, Rost B, Hunt J Montelione GT. Comparison of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc 2005;127:16505-16511.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 16505-16511
-
-
Snyder, D.A.1
Chen, Y.2
Denissova, N.G.3
Acton, T.4
Aramini, J.M.5
Ciano, M.6
Karlin, R.7
Liu, J.8
Manor, P.9
Rajan, P.A.10
Rossi, P.11
Swapna, G.V.T.12
Xiao, R.13
Rost, B.14
Hunt, J.15
Montelione, G.T.16
-
11
-
-
19544370676
-
Crystal packing effects on protein loops
-
Rapp CS, Pollack R. Crystal packing effects on protein loops. Proteins 2005;60:103-109.
-
(2005)
Proteins
, vol.60
, pp. 103-109
-
-
Rapp, C.S.1
Pollack, R.2
-
12
-
-
19544370004
-
Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures
-
Garbuzynskiy SO, Bogdan SM, Lobabov MY, Finkelstein AV, Galzitskaya OV. Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures. Proteins 2005;60:139-147.
-
(2005)
Proteins
, vol.60
, pp. 139-147
-
-
Garbuzynskiy, S.O.1
Bogdan, S.M.2
Lobabov, M.Y.3
Finkelstein, A.V.4
Galzitskaya, O.V.5
-
13
-
-
0037035520
-
The NMR analysis of the monomeric form of a mutant unliganded Bovine Neurophysin: Comparison with the crystal structure of a neurophysin dimer
-
Nguyen TL, Breslow E. The NMR analysis of the monomeric form of a mutant unliganded Bovine Neurophysin: comparison with the crystal structure of a neurophysin dimer. Biochemistry 2002;41:5920-5930.
-
(2002)
Biochemistry
, vol.41
, pp. 5920-5930
-
-
Nguyen, T.L.1
Breslow, E.2
-
14
-
-
0036160702
-
The NMR solution structure of the isolated Apo Pin1 WW domain: Comparison to the x-ray crystal structures of Pin1
-
Kowalski JA, Liu K, Kelly JW. The NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1. Biopolymers 2002;63:111-121.
-
(2002)
Biopolymers
, vol.63
, pp. 111-121
-
-
Kowalski, J.A.1
Liu, K.2
Kelly, J.W.3
-
16
-
-
0032493714
-
Quality assessment of NMR structures: A statistical survey
-
Doreleijers JF, Rullmann JAC, Kaptein R. Quality assessment of NMR structures: a statistical survey. J Mol Biol 1998;281:149-164.
-
(1998)
J Mol Biol
, vol.281
, pp. 149-164
-
-
Doreleijers, J.F.1
Rullmann, J.A.C.2
Kaptein, R.3
-
18
-
-
18844433630
-
Assessing precision and accuracy of protein structures derived from NMR data
-
Snyder DA. Assessing precision and accuracy of protein structures derived from NMR data. Proteins 2005;59:655-651.
-
(2005)
Proteins
, vol.59
, pp. 655-651
-
-
Snyder, D.A.1
-
19
-
-
3543012707
-
Crystallography and NMR system: A new software suite for macromolecular structure determination
-
Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
-
(1998)
Acta Crystallogr D Biol Crystallogr
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
20
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Guntert P, Mumenthaler C, Wutrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
-
(1997)
J Mol Biol
, vol.273
, pp. 283-298
-
-
Guntert, P.1
Mumenthaler, C.2
Wutrich, K.3
-
21
-
-
0037441524
-
Refinement of protein structures in explicit solvent
-
Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M. Refinement of protein structures in explicit solvent. Proteins 2003;50:496-506.
-
(2003)
Proteins
, vol.50
, pp. 496-506
-
-
Linge, J.P.1
Williams, M.A.2
Spronk, C.A.3
Bonvin, A.M.4
Nilges, M.5
-
22
-
-
0036234027
-
Comparison of solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model and with explicit water
-
Xia B, Tsui V, Case DA, Dyson HJ, Wright PE. Comparison of solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model and with explicit water. J Biomol NMR 2002;22:317-331.
-
(2002)
J Biomol NMR
, vol.22
, pp. 317-331
-
-
Xia, B.1
Tsui, V.2
Case, D.A.3
Dyson, H.J.4
Wright, P.E.5
-
23
-
-
10344226224
-
Refinement of NMR structures using implicit solvent and advanced sampling techniques
-
Chen J, Wonpil I, Brooks CL. Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc 2004;126:16038-16047.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 16038-16047
-
-
Chen, J.1
Wonpil, I.2
Brooks, C.L.3
-
24
-
-
2442610955
-
DRESS: A database of refined solution NMR structures
-
Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AMJJ, Vuister GW, Vriend G, Spronk AEM. DRESS: a database of refined solution NMR structures. Proteins 2004;55:483-486.
-
(2004)
Proteins
, vol.55
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Vranken, W.3
Doreleijers, J.F.4
Bonvin, A.M.J.J.5
Vuister, G.W.6
Vriend, G.7
Spronk, A.E.M.8
-
25
-
-
33645790319
-
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLOS
-
Nabuurs SB, Sprink CAEM, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLOS Comp Biol 2006;2:71-79.
-
(2006)
Comp Biol
, vol.2
, pp. 71-79
-
-
Nabuurs, S.B.1
Sprink, C.A.E.M.2
Vuister, G.W.3
Vriend, G.4
-
26
-
-
0037357143
-
The precision of NMR structure ensembles revisited
-
Spronk CAEM, Nabuurs SB, Bonvin AMJJ, Krieger E, Vuister GW, Vriend G. The precision of NMR structure ensembles revisited. J Biomol NMR 2003;25:225-234.
-
(2003)
J Biomol NMR
, vol.25
, pp. 225-234
-
-
Spronk, C.A.E.M.1
Nabuurs, S.B.2
Bonvin, A.M.J.J.3
Krieger, E.4
Vuister, G.W.5
Vriend, G.6
-
27
-
-
0034388123
-
Rapid determination of protein folds using residual dipolar couplings
-
Fowler CA, Tian F, Al-Hashimi HM, Prestegard JH. Rapid determination of protein folds using residual dipolar couplings. J Mol Biol 2000;304:447-460.
-
(2000)
J Mol Biol
, vol.304
, pp. 447-460
-
-
Fowler, C.A.1
Tian, F.2
Al-Hashimi, H.M.3
Prestegard, J.H.4
-
28
-
-
0346103679
-
Rapid protein fold determination using unassigned NMR data
-
Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci USA 2003;100:15404-15409.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15404-15409
-
-
Meiler, J.1
Baker, D.2
-
29
-
-
0032613288
-
Ab initio folding of proteins using restraints derived from evolutionary information
-
Ortiz AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins 1999;37 (Suppl 3):177-185.
-
(1999)
Proteins
, vol.37
, Issue.SUPPL. 3
, pp. 177-185
-
-
Ortiz, A.R.1
Kolinski, A.2
Rotkiewicz, P.3
Ilkowski, B.4
Skolnick, J.5
-
30
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118:11225-11236.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
31
-
-
0035913529
-
Evaluation and reparameterization of the OPLS-AA force field for protein via comparison with accurate quantum mechanical calculations on peptides
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparameterization of the OPLS-AA force field for protein via comparison with accurate quantum mechanical calculations on peptides. J Phys Chem B 2001;105:6474-6487.
-
(2001)
J Phys Chem B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
32
-
-
0001246294
-
Generalized Born model based on a surface integral formulation
-
Ghosh A, Rapp CS, Friesner RA. Generalized Born model based on a surface integral formulation. J Phys Chem B 1998;102:10983-10990.
-
(1998)
J Phys Chem B
, vol.102
, pp. 10983-10990
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
33
-
-
4344698912
-
Automated NMR protein structure calculation
-
Guntert P. Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectr 2003;43:105-125.
-
(2003)
Prog Nucl Magn Reson Spectr
, vol.43
, pp. 105-125
-
-
Guntert, P.1
|