-
1
-
-
0000408083
-
Mathematical procedure for superimposing atomic coordinates of proteins
-
McLachlan, A. D. 1972. Mathematical procedure for superimposing atomic coordinates of proteins. Acta Crystallogr. A. 28:656-657.
-
(1972)
Acta Crystallogr. A
, vol.28
, pp. 656-657
-
-
McLachlan, A.D.1
-
2
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A. 32:922-923.
-
(1976)
Acta Crystallogr. A
, vol.32
, pp. 922-923
-
-
Kabsch, W.1
-
3
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
Kabsch, W. 1978. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A. 34:827-828.
-
(1978)
Acta Crystallogr. A
, vol.34
, pp. 827-828
-
-
Kabsch, W.1
-
4
-
-
84948502362
-
Superposition of molecular structures using quaternions
-
Kneller, G. R. 1991. Superposition of molecular structures using quaternions. Mol. Simul. 7:113-119.
-
(1991)
Mol. Simul
, vol.7
, pp. 113-119
-
-
Kneller, G.R.1
-
5
-
-
27844494830
-
-
Kneller, G. R. 2005. Comment on Using quaternions to calculate RMSD [J. Comp. Chem. 25, 1849 (2004)]. J. Comput. Chem. 26:1660-1662.
-
Kneller, G. R. 2005. Comment on "Using quaternions to calculate RMSD" [J. Comp. Chem. 25, 1849 (2004)]. J. Comput. Chem. 26:1660-1662.
-
-
-
-
6
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
7
-
-
0032584783
-
Reversible peptide folding in solution by molecular dynamics simulation
-
Daura, X., B. Jaun, ..., A. E. Mark. 1998. Reversible peptide folding in solution by molecular dynamics simulation. J. Mol. Biol. 280:925-932.
-
(1998)
J. Mol. Biol
, vol.280
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Mark, A.E.3
-
8
-
-
0033557181
-
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations
-
Daura, X., W. F. van Gunsteren, and A. E. Mark. 1999. Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins. 34:269-280.
-
(1999)
Proteins
, vol.34
, pp. 269-280
-
-
Daura, X.1
van Gunsteren, W.F.2
Mark, A.E.3
-
9
-
-
0035850758
-
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic, B., E. J. Sorin, and V. Pande. 2001. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313:151-169.
-
(2001)
J. Mol. Biol
, vol.313
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.3
-
10
-
-
0036428782
-
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwidedistributed computing
-
Zagrovic, B., C. D. Snow, ..., V. S. Pande. 2002. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwidedistributed computing. J. Mol. Biol. 323:927-937.
-
(2002)
J. Mol. Biol
, vol.323
, pp. 927-937
-
-
Zagrovic, B.1
Snow, C.D.2
Pande, V.S.3
-
11
-
-
33846104376
-
All-atom ab initio folding of a diverse set of proteins
-
Yang, J. S., W. W. Chen, ..., E. I. Shakhnovich. 2007. All-atom ab initio folding of a diverse set of proteins. Structure. 15:53-63.
-
(2007)
Structure
, vol.15
, pp. 53-63
-
-
Yang, J.S.1
Chen, W.W.2
Shakhnovich, E.I.3
-
12
-
-
67650354848
-
A free-energy approach for all-atom protein simulation
-
Verma, A., and W. Wenzel. 2009. A free-energy approach for all-atom protein simulation. Biophys. J. 96:3483-3494.
-
(2009)
Biophys. J
, vol.96
, pp. 3483-3494
-
-
Verma, A.1
Wenzel, W.2
-
13
-
-
27344449197
-
Progress in modeling of protein structures and interactions
-
Schueler-Furman, O., C. Wang, ..., D. Baker. 2005. Progress in modeling of protein structures and interactions. Science. 310:638-642.
-
(2005)
Science
, vol.310
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Baker, D.3
-
14
-
-
47349085903
-
fRMSDPred: Predicting local RMSD between structural fragments using sequence information
-
Rangwala, H., and G. Karypis. 2008. fRMSDPred: predicting local RMSD between structural fragments using sequence information. Proteins. 72:1005-1018.
-
(2008)
Proteins
, vol.72
, pp. 1005-1018
-
-
Rangwala, H.1
Karypis, G.2
-
15
-
-
44949145113
-
Progress and challenges in protein structure prediction
-
Zhang, Y. 2008. Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol. 18:342-348.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 342-348
-
-
Zhang, Y.1
-
16
-
-
67649203376
-
The roles of entropy and kinetics in structure prediction
-
Bowman, G. R., and V. S. Pande. 2009. The roles of entropy and kinetics in structure prediction. PLoS One. 4:e5840.
-
(2009)
PLoS One
, vol.4
-
-
Bowman, G.R.1
Pande, V.S.2
-
17
-
-
35448929112
-
A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing
-
Andrec, M., D. A. Snyder, ..., R. M. Levy. 2007. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins. 69:449-465.
-
(2007)
Proteins
, vol.69
, pp. 449-465
-
-
Andrec, M.1
Snyder, D.A.2
Levy, R.M.3
-
18
-
-
52049100956
-
The war of tools: How can NMRspectroscopists detect errors in their structures?
-
Saccenti, E., and A. Rosato. 2008. The war of tools: how can NMRspectroscopists detect errors in their structures? J. Biomol. NMR. 40:251-261.
-
(2008)
J. Biomol. NMR
, vol.40
, pp. 251-261
-
-
Saccenti, E.1
Rosato, A.2
-
19
-
-
0035283159
-
Conformation spaces of proteins
-
Sullivan, D. C., and I. D. Kuntz. 2001. Conformation spaces of proteins. Proteins. 42:495-511.
-
(2001)
Proteins
, vol.42
, pp. 495-511
-
-
Sullivan, D.C.1
Kuntz, I.D.2
-
20
-
-
3042730828
-
Distributions in protein conformation space: Implications for structure prediction and entropy
-
Sullivan, D. C., and I. D. Kuntz. 2004. Distributions in protein conformation space: implications for structure prediction and entropy. Biophys. J. 87:113-120.
-
(2004)
Biophys. J
, vol.87
, pp. 113-120
-
-
Sullivan, D.C.1
Kuntz, I.D.2
-
21
-
-
67249132371
-
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble
-
Müller, C. L., I. F. Sbalzarini, ..., P. H. Hünenberger. 2009. In the eye of the beholder: inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. J. Chem. Phys. 130:214904-214925.
-
(2009)
J. Chem. Phys
, vol.130
, pp. 214904-214925
-
-
Müller, C.L.1
Sbalzarini, I.F.2
Hünenberger, P.H.3
-
22
-
-
0037230925
-
Efficient RMSD measures for the comparison of two molecular ensembles
-
Brüschweiler, R. 2003. Efficient RMSD measures for the comparison of two molecular ensembles. Proteins. 50:26-34.
-
(2003)
Proteins
, vol.50
, pp. 26-34
-
-
Brüschweiler, R.1
-
23
-
-
35048876171
-
Computational analysis of the mechanism and thermodynamics of inhibition of phosphodiesterase 5A by synthetic ligands
-
Zagrovic, B., and W. F. van Gunsteren. 2007. Computational analysis of the mechanism and thermodynamics of inhibition of phosphodiesterase 5A by synthetic ligands. J. Chem. Theory Comput. 3:301-311.
-
(2007)
J. Chem. Theory Comput
, vol.3
, pp. 301-311
-
-
Zagrovic, B.1
van Gunsteren, W.F.2
-
24
-
-
0035882568
-
Solution structure and dynamics of ribonuclease Sa
-
Laurents, D., J. M. Pérez-Cañadillas, ..., M. Bruix. 2001. Solution structure and dynamics of ribonuclease Sa. Proteins. 44:200-211.
-
(2001)
Proteins
, vol.44
, pp. 200-211
-
-
Laurents, D.1
Pérez-Cañadillas, J.M.2
Bruix, M.3
-
25
-
-
44349186057
-
The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition
-
Kövér, K. E., M. Bruix, ..., M. Rico. 2008. The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition. J. Mol. Biol. 379:953-965.
-
(2008)
J. Mol. Biol
, vol.379
, pp. 953-965
-
-
Kövér, K.E.1
Bruix, M.2
Rico, M.3
-
26
-
-
84954358515
-
The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H
-
Zhou, Z., H. Q. Feng, ..., Y. Bai. 2008. The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H. J. Mol. Biol. 384:531-539.
-
(2008)
J. Mol. Biol
, vol.384
, pp. 531-539
-
-
Zhou, Z.1
Feng, H.Q.2
Bai, Y.3
-
27
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle, D., K. T. Simons, and D. Baker. 1998. Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. USA. 95:11158-11162.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
28
-
-
0000467663
-
Finding the needle in a haystack: Educing native folds from ambiguous ab initio protein structure predictions
-
Betancourt, M. R., and J. Skolnick. 2001. Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. J. Comput. Chem. 22:339-353.
-
(2001)
J. Comput. Chem
, vol.22
, pp. 339-353
-
-
Betancourt, M.R.1
Skolnick, J.2
-
29
-
-
1942519275
-
SPICKER: A clustering approach to identify near-native protein folds
-
Zhang, Y., and J. Skolnick. 2004. SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem. 25:865-871.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
30
-
-
17844408143
-
Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction
-
Kró l, M., I. Roterman, ..., P. Spólnik. 2005. Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction. Proteins. 59:545-554.
-
(2005)
Proteins
, vol.59
, pp. 545-554
-
-
Kró l, M.1
Roterman, I.2
Spólnik, P.3
-
31
-
-
28944453304
-
Barnase thermal titration via molecular dynamics simulations: Detection of early denaturation sites
-
Yin, J., D. Bowen, and W. M. Southerland. 2006. Barnase thermal titration via molecular dynamics simulations: detection of early denaturation sites. J. Mol. Graph. Model. 24:233-243.
-
(2006)
J. Mol. Graph. Model
, vol.24
, pp. 233-243
-
-
Yin, J.1
Bowen, D.2
Southerland, W.M.3
-
32
-
-
65249179022
-
Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme
-
Sousa, S. F., P. A. Fernandes, and M. J. Ramos. 2009. Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme. Bioorg. Med. Chem. 17:3369-3378.
-
(2009)
Bioorg. Med. Chem
, vol.17
, pp. 3369-3378
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
34
-
-
0025037796
-
Comparison of the dynamics of myoglobin in different crystal forms
-
Phillips, Jr., G. N. 1990. Comparison of the dynamics of myoglobin in different crystal forms. Biophys. J. 57:381-383.
-
(1990)
Biophys. J
, vol.57
, pp. 381-383
-
-
Phillips Jr., G.N.1
-
35
-
-
0037022347
-
Flexibility and packing in proteins
-
Halle, B. 2002. Flexibility and packing in proteins. Proc. Natl. Acad. Sci. USA. 99:1274-1279.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1274-1279
-
-
Halle, B.1
-
36
-
-
22144482668
-
Fluctuations and correlations in crystalline protein dynamics: A simulation analysis of staphylococcal nuclease
-
Meinhold, L., and J. C. Smith. 2005. Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys. J. 88:2554-2563.
-
(2005)
Biophys. J
, vol.88
, pp. 2554-2563
-
-
Meinhold, L.1
Smith, J.C.2
-
37
-
-
30344438241
-
Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure
-
Lu, W. C., C. Z. Wang, ..., K. M. Ho. 2006. Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure. Proteins. 62:152-158.
-
(2006)
Proteins
, vol.62
, pp. 152-158
-
-
Lu, W.C.1
Wang, C.Z.2
Ho, K.M.3
-
38
-
-
34249061686
-
On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement
-
Glykos, N. M. 2007. On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 63:705-713.
-
(2007)
Acta Crystallogr. D Biol. Crystallogr
, vol.63
, pp. 705-713
-
-
Glykos, N.M.1
-
39
-
-
34249945151
-
Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions
-
Yang, L. W., E. Eyal, ..., I. Bahar. 2007. Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions. Structure. 15:741-749.
-
(2007)
Structure
, vol.15
, pp. 741-749
-
-
Yang, L.W.1
Eyal, E.2
Bahar, I.3
-
40
-
-
46449098635
-
On the relationship between the protein structure and protein dynamics
-
Lu, C. H., S. W. Huang, ..., J. K. Hwang. 2008. On the relationship between the protein structure and protein dynamics. Proteins. 72: 625-634.
-
(2008)
Proteins
, vol.72
, pp. 625-634
-
-
Lu, C.H.1
Huang, S.W.2
Hwang, J.K.3
-
41
-
-
67649412163
-
All-atom contact model for understanding protein dynamics from crystallographic B-factors
-
Li, D. W., and R. Brüschweiler. 2009. All-atom contact model for understanding protein dynamics from crystallographic B-factors. Biophys. J. 96:3074-3081.
-
(2009)
Biophys. J
, vol.96
, pp. 3074-3081
-
-
Li, D.W.1
Brüschweiler, R.2
-
42
-
-
76149086139
-
-
Hu, Z., and J. Jiang. 2010. Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal. J. Comp. Chem. 31:371-380.
-
Hu, Z., and J. Jiang. 2010. Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal. J. Comp. Chem. 31:371-380.
-
-
-
-
43
-
-
0021918946
-
Prediction of chain flexibility in proteins - a tool for the selection of peptide antigens
-
Karplus, P. A., and G. E. Schulz. 1985. Prediction of chain flexibility in proteins - a tool for the selection of peptide antigens. Naturwissenschaften. 72:212-213.
-
(1985)
Naturwissenschaften
, vol.72
, pp. 212-213
-
-
Karplus, P.A.1
Schulz, G.E.2
-
44
-
-
0028361031
-
Accuracy of protein flexibility predictions
-
Vihinen, M., E. Torkkila, and P. Riikonen. 1994. Accuracy of protein flexibility predictions. Proteins. 19:141-149.
-
(1994)
Proteins
, vol.19
, pp. 141-149
-
-
Vihinen, M.1
Torkkila, E.2
Riikonen, P.3
-
45
-
-
0023557882
-
Relationship of protein flexibility to thermostability
-
Vihinen, M. 1987. Relationship of protein flexibility to thermostability. Protein Eng. 1:477-480.
-
(1987)
Protein Eng
, vol.1
, pp. 477-480
-
-
Vihinen, M.1
-
46
-
-
0033955909
-
Protein thermal stability: Insights from atomic displacement parameters (B values)
-
Parthasarathy, S., and M. R. N. Murthy. 2000. Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng. 13:9-13.
-
(2000)
Protein Eng
, vol.13
, pp. 9-13
-
-
Parthasarathy, S.1
Murthy, M.R.N.2
-
47
-
-
65349143121
-
Knowledge-guided laboratory evolution of protein thermolability
-
Reetz, M. T., P. Soni, and L. Fernández. 2009. Knowledge-guided laboratory evolution of protein thermolability. Biotechnol. Bioeng. 102:1712-1717.
-
(2009)
Biotechnol. Bioeng
, vol.102
, pp. 1712-1717
-
-
Reetz, M.T.1
Soni, P.2
Fernández, L.3
-
48
-
-
0028883878
-
Significance of structural changes in proteins: Expected errors in refined protein structures
-
Stroud, R. M., and E. B. Fauman. 1995. Significance of structural changes in proteins: expected errors in refined protein structures. Protein Sci. 4:2392-2404.
-
(1995)
Protein Sci
, vol.4
, pp. 2392-2404
-
-
Stroud, R.M.1
Fauman, E.B.2
-
49
-
-
0032080521
-
Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors
-
Carugo, O., and P. Argos. 1998. Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors. Proteins. 31:201-213.
-
(1998)
Proteins
, vol.31
, pp. 201-213
-
-
Carugo, O.1
Argos, P.2
-
50
-
-
0037316987
-
Flexibility analysis of enzyme active sites by crystallographic temperature factors
-
Yuan, Z., J. Zhao, and Z. X. Wang. 2003. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng. 16:109-114.
-
(2003)
Protein Eng
, vol.16
, pp. 109-114
-
-
Yuan, Z.1
Zhao, J.2
Wang, Z.X.3
-
51
-
-
0242385341
-
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: An insight into the molecular basis of antibody cross-reactivity and specificity
-
Mohan, S., N. Sinha, and S. J. Smith-Gill. 2003. Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity. Biophys. J. 85:3221-3236.
-
(2003)
Biophys. J
, vol.85
, pp. 3221-3236
-
-
Mohan, S.1
Sinha, N.2
Smith-Gill, S.J.3
-
52
-
-
0030853145
-
Correlation between side chain mobility and conformation in protein structures
-
Carugo, O., and P. Argos. 1997. Correlation between side chain mobility and conformation in protein structures. Protein Eng. 10:777-787.
-
(1997)
Protein Eng
, vol.10
, pp. 777-787
-
-
Carugo, O.1
Argos, P.2
-
53
-
-
0037296382
-
Protein side-chain rearrangement in regions of point mutations
-
Eyal, E., R. Najmanovich, ..., V. Sobolev. 2003. Protein side-chain rearrangement in regions of point mutations. Proteins. 50:272-282.
-
(2003)
Proteins
, vol.50
, pp. 272-282
-
-
Eyal, E.1
Najmanovich, R.2
Sobolev, V.3
-
54
-
-
0030850230
-
Protein-protein crystal-packing contacts
-
Carugo, O., and P. Argos. 1997. Protein-protein crystal-packing contacts. Protein Sci. 6:2261-2263.
-
(1997)
Protein Sci
, vol.6
, pp. 2261-2263
-
-
Carugo, O.1
Argos, P.2
-
55
-
-
0028119988
-
Compositional characteristics of relatively disordered regions in proteins
-
Altman, R., C. Hughes, ..., O. Jardetsky. 1994. Compositional characteristics of relatively disordered regions in proteins. Protein Pept. Lett. 1:120-127.
-
(1994)
Protein Pept. Lett
, vol.1
, pp. 120-127
-
-
Altman, R.1
Hughes, C.2
Jardetsky, O.3
-
56
-
-
0030691703
-
Identifying disordered regions in proteins from amino acid sequence
-
Houston, TX
-
Romero, P., Z. Obradovic, ..., A. K. Dunker. 1997. Identifying disordered regions in proteins from amino acid sequence. The 1997 IEEE International Conference on Neural Networks Proc, Houston, TX. 1:90-95.
-
(1997)
The 1997 IEEE International Conference on Neural Networks Proc
, vol.1
, pp. 90-95
-
-
Romero, P.1
Obradovic, Z.2
Dunker, A.K.3
-
57
-
-
0031633365
-
Thousands of proteins likely to have long disordered regions
-
Romero, P., Z. Obradovic, ..., A. K. Dunker. 1998. Thousands of proteins likely to have long disordered regions. Pac. Symp. Biocomput. 3:437-448.
-
(1998)
Pac. Symp. Biocomput
, vol.3
, pp. 437-448
-
-
Romero, P.1
Obradovic, Z.2
Dunker, A.K.3
-
59
-
-
1042291214
-
Myosin flexibility: Structural domains and collective vibrations
-
Navizet, I., R. Lavery, and R. L. Jernigan. 2004. Myosin flexibility: structural domains and collective vibrations. Proteins. 54:384-393.
-
(2004)
Proteins
, vol.54
, pp. 384-393
-
-
Navizet, I.1
Lavery, R.2
Jernigan, R.L.3
-
60
-
-
0025904209
-
Rigid protein motion as a model for crystallographic temperature factors
-
Kuriyan, J., and W. I. Weis. 1991. Rigid protein motion as a model for crystallographic temperature factors. Proc. Natl. Acad. Sci. USA. 88:2773-2777.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 2773-2777
-
-
Kuriyan, J.1
Weis, W.I.2
-
61
-
-
0018793861
-
Temperaturedependent x-ray diffraction as a probe of protein structural dynamics
-
Frauenfelder, H., G. A. Petsko, and D. Tsernoglou. 1979. Temperaturedependent x-ray diffraction as a probe of protein structural dynamics. Nature. 280:558-563.
-
(1979)
Nature
, vol.280
, pp. 558-563
-
-
Frauenfelder, H.1
Petsko, G.A.2
Tsernoglou, D.3
-
62
-
-
0034833358
-
Dynamical transition of myoglobin in a crystal: Comparative studies of x-ray crystallography and Mössbauer spectroscopy
-
Chong, S. H., Y. Joti, ..., F. Parak. 2001. Dynamical transition of myoglobin in a crystal: comparative studies of x-ray crystallography and Mössbauer spectroscopy. Eur. Biophys. J. 30:319-329.
-
(2001)
Eur. Biophys. J
, vol.30
, pp. 319-329
-
-
Chong, S.H.1
Joti, Y.2
Parak, F.3
-
63
-
-
34547679071
-
NMR: Prediction of protein flexibility
-
Berjanskii, M., and D. S. Wishart. 2006. NMR: prediction of protein flexibility. Nat. Protoc. 1:683-688.
-
(2006)
Nat. Protoc
, vol.1
, pp. 683-688
-
-
Berjanskii, M.1
Wishart, D.S.2
-
64
-
-
34547563370
-
The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts
-
35(Web Server issue):W531-W537
-
Berjanskii, M. V., and D. S. Wishart. 2007. The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res. 35(Web Server issue):W531-W537.
-
(2007)
Nucleic Acids Res
-
-
Berjanskii, M.V.1
Wishart, D.S.2
-
65
-
-
37848999781
-
Application of the random coil index to studying protein flexibility
-
Berjanskii, M. V., and D. S. Wishart. 2008. Application of the random coil index to studying protein flexibility. J. Biomol. NMR. 40:31-48.
-
(2008)
J. Biomol. NMR
, vol.40
, pp. 31-48
-
-
Berjanskii, M.V.1
Wishart, D.S.2
-
66
-
-
0031058410
-
NMRstructure of the 35-residue villin headpiece subdomain
-
McKnight, C. J., P. T. Matsudaira, and P. S. Kim. 1997.NMRstructure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4:180-184.
-
(1997)
Nat. Struct. Biol
, vol.4
, pp. 180-184
-
-
McKnight, C.J.1
Matsudaira, P.T.2
Kim, P.S.3
-
67
-
-
0028884580
-
The radius of gyration of an apomyoglobin folding intermediate
-
Eliezer, D., P. A. Jennings, ..., H. Tsuruta. 1995. The radius of gyration of an apomyoglobin folding intermediate. Science. 270:487-488.
-
(1995)
Science
, vol.270
, pp. 487-488
-
-
Eliezer, D.1
Jennings, P.A.2
Tsuruta, H.3
-
68
-
-
0035163689
-
Predicting properties of intrinsically unstructured proteins
-
Bright, J. N., T. B. Woolf, and J. H. Hoh. 2001. Predicting properties of intrinsically unstructured proteins. Prog. Biophys. Mol. Biol. 76: 131-173.
-
(2001)
Prog. Biophys. Mol. Biol
, vol.76
, pp. 131-173
-
-
Bright, J.N.1
Woolf, T.B.2
Hoh, J.H.3
-
69
-
-
33749027499
-
Criteria for downhill protein folding: Calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity
-
Knott, M., and H. S. Chan. 2006. Criteria for downhill protein folding: calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity. Proteins. 65:373-391.
-
(2006)
Proteins
, vol.65
, pp. 373-391
-
-
Knott, M.1
Chan, H.S.2
-
71
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu, D., P. S. Shenkin, ..., W. C. Still. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. 101:3005-3014.
-
(1997)
J. Phys. Chem
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Still, W.C.3
-
72
-
-
48749148224
-
Rattle - a velocity version of the shake algorithm for molecular-dynamics calculations
-
Andersen, H. C. 1983. Rattle - a velocity version of the shake algorithm for molecular-dynamics calculations. J. Comput. Phys. 52:24-34.
-
(1983)
J. Comput. Phys
, vol.52
, pp. 24-34
-
-
Andersen, H.C.1
-
73
-
-
33645941402
-
The Opls potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin
-
Jorgensen, W. L., and J. Tiradorives. 1988. The Opls potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
-
(1988)
J. Am. Chem. Soc
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tiradorives, J.2
-
74
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
Zagrovic, B., C. D. Snow, ..., V. S. Pande. 2002. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323:153-164.
-
(2002)
J. Mol. Biol
, vol.323
, pp. 153-164
-
-
Zagrovic, B.1
Snow, C.D.2
Pande, V.S.3
-
75
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
76
-
-
0000009443
-
Rapid comparison of protein structures
-
McLachlan, A. D. 1982. Rapid comparison of protein structures. Acta Crystallogr. A. 38:871-873.
-
(1982)
Acta Crystallogr. A
, vol.38
, pp. 871-873
-
-
McLachlan, A.D.1
-
77
-
-
33644807131
-
Is one solution good enough?
-
discussion 185
-
Furnham, N., T. L. Blundell, ..., T. C. Terwilliger. 2006. Is one solution good enough? Nat. Struct. Mol. Biol. 13:184-185, discussion 185.
-
(2006)
Nat. Struct. Mol. Biol
, vol.13
, pp. 184-185
-
-
Furnham, N.1
Blundell, T.L.2
Terwilliger, T.C.3
-
78
-
-
34250874462
-
Multiple structure alignment by optimal RMSD implies that the average structure is a consensus
-
Stanford, CA
-
Wang, X., and J. Snoeyink. 2006. Multiple structure alignment by optimal RMSD implies that the average structure is a consensus. LSS Computational Systems Bioinformatics Conference, Stanford, CA. 79-87.
-
(2006)
LSS Computational Systems Bioinformatics Conference
, pp. 79-87
-
-
Wang, X.1
Snoeyink, J.2
-
79
-
-
0035028578
-
Assessing the effect of conformational averaging on the measured values of observables
-
Bürgi, R., J. Pitera, and W. F. van Gunsteren. 2001. Assessing the effect of conformational averaging on the measured values of observables. J. Biomol. NMR. 19:305-320.
-
(2001)
J. Biomol. NMR
, vol.19
, pp. 305-320
-
-
Bürgi, R.1
Pitera, J.2
van Gunsteren, W.F.3
-
80
-
-
33645033314
-
Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?
-
Zagrovic, B., and W. F. van Gunsteren. 2006. Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us? Proteins. 63:210-218.
-
(2006)
Proteins
, vol.63
, pp. 210-218
-
-
Zagrovic, B.1
van Gunsteren, W.F.2
-
81
-
-
58849160465
-
Re-refinement from deposited x-ray data can deliver improved models for most PDB entries
-
Joosten, R. P., T. Womack, ..., G. Bricogne. 2009. Re-refinement from deposited x-ray data can deliver improved models for most PDB entries. Acta Crystallogr. D Biol. Crystallogr. 65:176-185.
-
(2009)
Acta Crystallogr. D Biol. Crystallogr
, vol.65
, pp. 176-185
-
-
Joosten, R.P.1
Womack, T.2
Bricogne, G.3
-
82
-
-
2442610955
-
DRESS: A database of REfined solution NMR structures
-
Nabuurs, S. B., A. J. Nederveen, ..., C. A. Spronk. 2004. DRESS: a database of REfined solution NMR structures. Proteins. 55:483-486.
-
(2004)
Proteins
, vol.55
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Spronk, C.A.3
-
83
-
-
34447498926
-
PDB improvement starts with data deposition
-
Joosten, R. P., and G. Vriend. 2007. PDB improvement starts with data deposition. Science. 317:195-196.
-
(2007)
Science
, vol.317
, pp. 195-196
-
-
Joosten, R.P.1
Vriend, G.2
|