-
1
-
-
0033954256
-
The protein data bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. 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
-
2
-
-
0035478854
-
Random forests
-
Breiman L. Random forests. Mach. Learn. 2001, 45:5-32.
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
3
-
-
0030853145
-
Correlation between side chain mobility and conformation in protein structures
-
Carugo O., Argos P. Correlation between side chain mobility and conformation in protein structures. Protein Eng. 1997, 10:777-787.
-
(1997)
Protein Eng.
, vol.10
, pp. 777-787
-
-
Carugo, O.1
Argos, P.2
-
4
-
-
0032080521
-
Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors
-
Carugo O., Argos P. Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors. Proteins 1998, 31:201-213.
-
(1998)
Proteins
, vol.31
, pp. 201-213
-
-
Carugo, O.1
Argos, P.2
-
5
-
-
33846965982
-
Prediction of protein B-factors using multi-class bounded SVM
-
Chen P., Wang B., Wong H.S., Huang D.S. Prediction of protein B-factors using multi-class bounded SVM. Protein Pept. Lett. 2007, 14:185-190.
-
(2007)
Protein Pept. Lett.
, vol.14
, pp. 185-190
-
-
Chen, P.1
Wang, B.2
Wong, H.S.3
Huang, D.S.4
-
6
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117:5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
7
-
-
0000053123
-
Protein flexibility in solution and in crystals
-
Eastman P., Pellegrini M., Doniach S. Protein flexibility in solution and in crystals. J. Chem. Phys. 1999, 110:10141-10152.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 10141-10152
-
-
Eastman, P.1
Pellegrini, M.2
Doniach, S.3
-
8
-
-
0037296382
-
Protein side-chain rearrangement in regions of point mutations
-
Eyal E., Najmanovich R., Edelman M., Sobolev V. Protein side-chain rearrangement in regions of point mutations. Proteins 2003, 50:272-282.
-
(2003)
Proteins
, vol.50
, pp. 272-282
-
-
Eyal, E.1
Najmanovich, R.2
Edelman, M.3
Sobolev, V.4
-
10
-
-
0037022347
-
Flexibility and packing in proteins
-
Halle B. Flexibility and packing in proteins. Proc. Natl. Acad. Sci. USA 2002, 99:1274-1279.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1274-1279
-
-
Halle, B.1
-
11
-
-
77951666362
-
Toward quantitative characterization of the binding profile between the human amphiphysin-1 SH3 domain and its peptide ligands
-
He P., Wu W., Wang H.D., Yang K., Liao K.L., Zhang W. Toward quantitative characterization of the binding profile between the human amphiphysin-1 SH3 domain and its peptide ligands. Amino Acids 2010, 38:1209-1218.
-
(2010)
Amino Acids
, vol.38
, pp. 1209-1218
-
-
He, P.1
Wu, W.2
Wang, H.D.3
Yang, K.4
Liao, K.L.5
Zhang, W.6
-
12
-
-
49449085241
-
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
-
Joung I.S., Cheatham T.E. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B 2008, 112:9020-9041.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
13
-
-
33745499790
-
Electron transfer between cofactors in protein domains linked by a flexible tether
-
Kawatsua T., Beratan D.N. Electron transfer between cofactors in protein domains linked by a flexible tether. Chem. Phys. 2006, 326:259-269.
-
(2006)
Chem. Phys.
, vol.326
, pp. 259-269
-
-
Kawatsua, T.1
Beratan, D.N.2
-
14
-
-
75649105430
-
Chloride ion conduction without water coordination in the pore of ClC protein
-
Ko Y.J., Jo W.H. Chloride ion conduction without water coordination in the pore of ClC protein. J. Comput. Chem. 2010, 31:603-611.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 603-611
-
-
Ko, Y.J.1
Jo, W.H.2
-
15
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov G.G., Shapovalov M.V., Dunbrack R.L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009, 77:778-795.
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack, R.L.3
-
16
-
-
0035996990
-
Dynamics of proteins in crystals: comparison of experiment with simple models
-
Kundu S., Melton J.S., Sorensen D.C., Phillips G.N. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys. J. 2002, 83:723-732.
-
(2002)
Biophys. J.
, vol.83
, pp. 723-732
-
-
Kundu, S.1
Melton, J.S.2
Sorensen, D.C.3
Phillips, G.N.4
-
17
-
-
0034663722
-
The penultimate rotamer library
-
Lovell S.C., Word J.M., Richardson J.S., Richardson D.C. The penultimate rotamer library. Proteins 2000, 40:389-408.
-
(2000)
Proteins
, vol.40
, pp. 389-408
-
-
Lovell, S.C.1
Word, J.M.2
Richardson, J.S.3
Richardson, D.C.4
-
18
-
-
1042291214
-
Myosin flexibility: structure domains and collective vibrations
-
Navizet I., Lavery R., Jernigan R.L. Myosin flexibility: structure domains and collective vibrations. Proteins 2004, 54:384-393.
-
(2004)
Proteins
, vol.54
, pp. 384-393
-
-
Navizet, I.1
Lavery, R.2
Jernigan, R.L.3
-
19
-
-
2142720593
-
Ion binding and ion specificity: the Hofmeister effect and Onsager and Lifshitz theories
-
Ninham B.W., Yaminsky V. Ion binding and ion specificity: the Hofmeister effect and Onsager and Lifshitz theories. Langmuir 1997, 13:2097-2108.
-
(1997)
Langmuir
, vol.13
, pp. 2097-2108
-
-
Ninham, B.W.1
Yaminsky, V.2
-
20
-
-
77952714180
-
Prediction of water's mobility and disorder in protein crystals using novel local hydrophobic descriptors
-
Pan Y., Lv F., Tian F., Luo X., Kong X., Li Y., Yang Q. Prediction of water's mobility and disorder in protein crystals using novel local hydrophobic descriptors. Mol. Inf. 2010, 29:195-201.
-
(2010)
Mol. Inf.
, vol.29
, pp. 195-201
-
-
Pan, Y.1
Lv, F.2
Tian, F.3
Luo, X.4
Kong, X.5
Li, Y.6
Yang, Q.7
-
21
-
-
73449096798
-
Robust prediction of B-factor profile from sequence using two-stage SVR based on random forest feature selection
-
Pan X.Y., Shen H.B. Robust prediction of B-factor profile from sequence using two-stage SVR based on random forest feature selection. Protein Pept. Lett. 2009, 16:1447-1454.
-
(2009)
Protein Pept. Lett.
, vol.16
, pp. 1447-1454
-
-
Pan, X.Y.1
Shen, H.B.2
-
22
-
-
0031439702
-
Analysis of temperature factor distribution in high-resolution protein structures
-
Parthasarathy S., Murthy M.R. Analysis of temperature factor distribution in high-resolution protein structures. Protein Sci. 1997, 6:2561-2567.
-
(1997)
Protein Sci.
, vol.6
, pp. 2561-2567
-
-
Parthasarathy, S.1
Murthy, M.R.2
-
23
-
-
0033955909
-
Protein thermal stability: insights from atomic displacement parameters (B values)
-
Parthasarathy S., Murthy M.R.N. Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng. 2000, 13:9-13.
-
(2000)
Protein Eng.
, vol.13
, pp. 9-13
-
-
Parthasarathy, S.1
Murthy, M.R.N.2
-
24
-
-
0347364621
-
Protein flexibility and intrinsic disorder
-
Radivojac P., Obradovic Z., Smith D.K., Zhu G., Vucetic S., Brown C.J., Lawson J.D., Dunker A.K. Protein flexibility and intrinsic disorder. Protein Sci. 2004, 13:71-80.
-
(2004)
Protein Sci.
, vol.13
, pp. 71-80
-
-
Radivojac, P.1
Obradovic, Z.2
Smith, D.K.3
Zhu, G.4
Vucetic, S.5
Brown, C.J.6
Lawson, J.D.7
Dunker, A.K.8
-
26
-
-
1642452918
-
Structural alteration of cofactor specificity in Corynebacterium 2, 5-diketo-d-gluconic acid reductase
-
Sanli G., Banta S., Anderson S., Blaber M. Structural alteration of cofactor specificity in Corynebacterium 2, 5-diketo-d-gluconic acid reductase. Protein Sci. 2004, 13:504-512.
-
(2004)
Protein Sci.
, vol.13
, pp. 504-512
-
-
Sanli, G.1
Banta, S.2
Anderson, S.3
Blaber, M.4
-
27
-
-
0033601299
-
Substitution of pyridoxal 5'-phosphate ind-serine dehydratase from Escherichia coli by cofactor analogues provides information on cofactor binding and catalysis
-
Schnackerz K.D., Tai C.H., Pötsch R.K.W., Cook P.F. Substitution of pyridoxal 5'-phosphate ind-serine dehydratase from Escherichia coli by cofactor analogues provides information on cofactor binding and catalysis. J. Biol. Chem. 1999, 274:36935-36943.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 36935-36943
-
-
Schnackerz, K.D.1
Tai, C.H.2
Pötsch, R.K.W.3
Cook, P.F.4
-
28
-
-
0037407015
-
Improved amino acid flexibility parameters
-
Smith D.K., Radivojac P., Obradovic Z., Dunker A.K., Zhu G. Improved amino acid flexibility parameters. Protein Sci. 2003, 12:1060-1072.
-
(2003)
Protein Sci.
, vol.12
, pp. 1060-1072
-
-
Smith, D.K.1
Radivojac, P.2
Obradovic, Z.3
Dunker, A.K.4
Zhu, G.5
-
29
-
-
0032638628
-
Least squares support vector machine classifiers
-
Suykens J.A.K., Vandewalle J. Least squares support vector machine classifiers. Neural Process. Lett. 1999, 9:293-300.
-
(1999)
Neural Process. Lett.
, vol.9
, pp. 293-300
-
-
Suykens, J.A.K.1
Vandewalle, J.2
-
30
-
-
65549154236
-
Predicting liquid chromatographic retention times of peptides from the Drosophila melanogaster proteome by machine learning approaches
-
Tian F., Yang L., Lv F., Zhou P. Predicting liquid chromatographic retention times of peptides from the Drosophila melanogaster proteome by machine learning approaches. Anal. Chim. Acta 2009, 644:10-16.
-
(2009)
Anal. Chim. Acta
, vol.644
, pp. 10-16
-
-
Tian, F.1
Yang, L.2
Lv, F.3
Zhou, P.4
-
31
-
-
67649945500
-
Modeling and prediction of retention behavior of histidine-containing peptides in immobilized metal-affinity chromatography
-
Tian F., Yang L., Lv F., Zhou P. Modeling and prediction of retention behavior of histidine-containing peptides in immobilized metal-affinity chromatography. J. Sep. Sci. 2009, 32:2159-2169.
-
(2009)
J. Sep. Sci.
, vol.32
, pp. 2159-2169
-
-
Tian, F.1
Yang, L.2
Lv, F.3
Zhou, P.4
-
32
-
-
0002518563
-
Knowledge-based B-factor restraints for the refinement of proteins
-
Tonrud D.E. Knowledge-based B-factor restraints for the refinement of proteins. J. Appl. Cryst. 1996, 29:100-104.
-
(1996)
J. Appl. Cryst.
, vol.29
, pp. 100-104
-
-
Tonrud, D.E.1
-
33
-
-
0023557882
-
Relationship of protein flexibility to thermostability
-
Vihinen M. Relationship of protein flexibility to thermostability. Protein Eng. 1987, 1:477-480.
-
(1987)
Protein Eng.
, vol.1
, pp. 477-480
-
-
Vihinen, M.1
-
34
-
-
0028361031
-
Accuracy of protein flexibility predictions
-
Vihinen M., Torkkila E., Riikonen P. Accuracy of protein flexibility predictions. Proteins 1994, 19:141-149.
-
(1994)
Proteins
, vol.19
, pp. 141-149
-
-
Vihinen, M.1
Torkkila, E.2
Riikonen, P.3
-
35
-
-
0031267176
-
Distribution analysis of the variation of B-factors of X-ray crystal structures; temperature and structural variations in lysozyme
-
Wampler J.E. Distribution analysis of the variation of B-factors of X-ray crystal structures; temperature and structural variations in lysozyme. J. Chem. Inf. Comput. Sci. 1997, 37:1171-1180.
-
(1997)
J. Chem. Inf. Comput. Sci.
, vol.37
, pp. 1171-1180
-
-
Wampler, J.E.1
-
37
-
-
0018107732
-
The conformational mobility of proteins and its functional significance
-
Williams R.J. The conformational mobility of proteins and its functional significance. Biochem. Soc. Trans. 1978, 6:1123-1126.
-
(1978)
Biochem. Soc. Trans.
, vol.6
, pp. 1123-1126
-
-
Williams, R.J.1
-
38
-
-
0033614004
-
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word J.M., Lovell S.C., Richardson J.S., Richardson D.C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 1999, 285:1735-1747.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
39
-
-
0037316987
-
Flexibility analysis of enzyme active sites by crystallographic temperature factors
-
Yuan Z., Zhao J., Wang Z.X. Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng. 2003, 16:109-114.
-
(2003)
Protein Eng.
, vol.16
, pp. 109-114
-
-
Yuan, Z.1
Zhao, J.2
Wang, Z.X.3
-
40
-
-
0028068802
-
Atomic-level accuracy in simulations of large protein crystals
-
York D.M., Wlodawer A., Pedersen L.G., Darden T.A. Atomic-level accuracy in simulations of large protein crystals. Proc. Natl. Acad. Sci. USA 1994, 91:8715-8718.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 8715-8718
-
-
York, D.M.1
Wlodawer, A.2
Pedersen, L.G.3
Darden, T.A.4
-
41
-
-
13944277320
-
Prediction of protein B-factor profiles
-
Yuan Z., Bailey T.L., Teasdale R.D. Prediction of protein B-factor profiles. Proteins 2005, 58:905-912.
-
(2005)
Proteins
, vol.58
, pp. 905-912
-
-
Yuan, Z.1
Bailey, T.L.2
Teasdale, R.D.3
-
42
-
-
66249145702
-
Geometrical characteristics of hydrogen bonds involving sulfur atoms in proteins
-
Zhou P., Tian F., Lv F., Zhang Z. Geometrical characteristics of hydrogen bonds involving sulfur atoms in proteins. Proteins 2009, 76:151-163.
-
(2009)
Proteins
, vol.76
, pp. 151-163
-
-
Zhou, P.1
Tian, F.2
Lv, F.3
Zhang, Z.4
-
43
-
-
62249165045
-
Comprehensive comparison of eight statistical modelling methods used in quantitative structure-retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome
-
Zhou P., Tian F., Lv F., Zhang Z. Comprehensive comparison of eight statistical modelling methods used in quantitative structure-retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome. J. Chromatogr. A 2009, 1216:3107-3116.
-
(2009)
J. Chromatogr. A
, vol.1216
, pp. 3107-3116
-
-
Zhou, P.1
Tian, F.2
Lv, F.3
Zhang, Z.4
-
44
-
-
78649525214
-
-
Halogen-ionic bridges: do they exist in the biomolecular world? J. Chem. Theory Comput., in press, doi:10.1021/ct100167w
-
Zhou, P., Ren, Y., Tian, F., Zou, J. Zhang, Z.. Halogen-ionic bridges: do they exist in the biomolecular world? J. Chem. Theory Comput., in press, doi:10.1021/ct100167w.
-
-
-
Zhou, P.1
Ren, Y.2
Tian, F.3
Zou, J.4
Zhang, Z.5
|