-
1
-
-
0032802062
-
On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
-
Amadei, A., M. A. Ceruso, and A. Di Nola. 1999. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins. 36:419-424.
-
(1999)
Proteins
, vol.36
, pp. 419-424
-
-
Amadei, A.1
Ceruso, M.A.2
Di Nola, A.3
-
2
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
3
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
4
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker, D., and A. Sali. 2001. Protein structure prediction and structural genomics. Science. 294:93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
5
-
-
0034127361
-
Collective protein dynamics in relation to function
-
Berendsen, H. J., and S. Hayward. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10:165-169.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 165-169
-
-
Berendsen, H.J.1
Hayward, S.2
-
6
-
-
0033977581
-
The ASTRAL compendium for protein structure and sequence analysis
-
Brenner, S. E., P. Koehl, and M. Levitt. 2000. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res. 28:254-256.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 254-256
-
-
Brenner, S.E.1
Koehl, P.2
Levitt, M.3
-
7
-
-
0032080528
-
Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
-
de Groot, B. L., S. Hayward, D, M. van Aalten, A. Amadei, and H. J. Berendsen. 1998. Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins. 31:116-127.
-
(1998)
Proteins
, vol.31
, pp. 116-127
-
-
Groot, B.L.1
Hayward, S.2
Van Aalten, D.M.3
Amadei, A.4
Berendsen, H.J.5
-
8
-
-
0036077875
-
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
-
Delarue, M., and Y. H. Sanejouand. 2002. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol. 320:1011-1024.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 1011-1024
-
-
Delarue, M.1
Sanejouand, Y.H.2
-
9
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
Ferrara, P., H. Gohlke, D. J. Price, G. Klebe, and C. L. Brooks 3rd. 2004. Assessing scoring functions for protein-ligand interactions. J. Med. Chem. 47:3032-3047.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3032-3047
-
-
Ferrara, P.1
Gohlke, H.2
Price, D.J.3
Klebe, G.4
Brooks III, C.L.5
-
10
-
-
0036283048
-
Evolution and physics in comparative protein structure modeling
-
Fiser, A., M. Feig, C. L. Brooks 3rd, and A. Sali. 2002. Evolution and physics in comparative protein structure modeling. Acc. Chem. Res. 35:413-421.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 413-421
-
-
Fiser, A.1
Feig, M.2
Brooks III, C.L.3
Sali, A.4
-
11
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
13
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-652.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
14
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley, L. A., R. M. MacCallum, and M. J. Sternberg. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299:499-520.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 499-520
-
-
Kelley, L.A.1
MacCallum, R.M.2
Sternberg, M.J.3
-
15
-
-
0035996975
-
Relating molecular flexibility to function: A case study of tubulin
-
Keskin, O., S. R. Durell, I. Bahar, R. L. Jernigan, and D. G. Covell. 2002. Relating molecular flexibility to function: a case study of tubulin, Biophys. J. 83:663-680.
-
(2002)
Biophys. J.
, vol.83
, pp. 663-680
-
-
Keskin, O.1
Durell, S.R.2
Bahar, I.3
Jernigan, R.L.4
Covell, D.G.5
-
16
-
-
0034029144
-
Proteins with similar architecture exhibit similar large-scale dynamic behavior
-
Keskin, O., R. L. Jernigan, and I. Bahar. 2000. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J. 78:2093-2106.
-
(2000)
Biophys. J.
, vol.78
, pp. 2093-2106
-
-
Keskin, O.1
Jernigan, R.L.2
Bahar, I.3
-
17
-
-
0033117937
-
Investigating protein dynamics in collective coordinate space
-
Kitao, A., and N. Go. 1999. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9:164-169.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 164-169
-
-
Kitao, A.1
Go, N.2
-
18
-
-
0043123211
-
EVA: Evaluation of protein structure prediction servers
-
Koh I. Y., V. A. Eyrich, M. A. Marti-Renom, D. Przybylski, M. S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, and B. Rost. 2003. EVA: evaluation of protein structure prediction servers. Nucleic Acids Res. 31:3311-3315.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3311-3315
-
-
Koh, I.Y.1
Eyrich, V.A.2
Marti-Renom, M.A.3
Przybylski, D.4
Madhusudhan, M.S.5
Eswar, N.6
Grana, O.7
Pazos, F.8
Valencia, A.9
Sali, A.10
Rost, B.11
-
19
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs, W. G., V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, and M. Gerstein. 2002. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48:682-695.
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
Alexandrov, V.2
Wilson, C.A.3
Echols, N.4
Yu, H.5
Gerstein, M.6
-
21
-
-
0030996005
-
Protein folding: The endgame
-
Levitt, M., M. Gerstein, E. Huang, S. Subbiah, and J. Tsai. 1997. Protein folding: the endgame. Annu. Rev. Biochem. 66:549-579.
-
(1997)
Annu. Rev. Biochem.
, vol.66
, pp. 549-579
-
-
Levitt, M.1
Gerstein, M.2
Huang, E.3
Subbiah, S.4
Tsai, J.5
-
22
-
-
1642365068
-
New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
-
Ma, J. 2004. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr. Protein Pept. Sci. 5:119-123.
-
(2004)
Curr. Protein Pept. Sci.
, vol.5
, pp. 119-123
-
-
Ma, J.1
-
23
-
-
1842559320
-
Alignment of protein sequences by their profiles
-
Marti-Renom, M. A., M. S. Madhusudhan, and A. Sali. 2004. Alignment of protein sequences by their profiles. Protein Sci. 13:1071-1087.
-
(2004)
Protein Sci.
, vol.13
, pp. 1071-1087
-
-
Marti-Renom, M.A.1
Madhusudhan, M.S.2
Sali, A.3
-
24
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom, M. A., A. C. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali. 2000. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29:291-325.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
25
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
26
-
-
0036839162
-
MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
-
Ortiz, A. R., C. E. Strauss, and O. Olmea. 2002. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 11:2606-2621.
-
(2002)
Protein Sci.
, vol.11
, pp. 2606-2621
-
-
Ortiz, A.R.1
Strauss, C.E.2
Olmea, O.3
-
27
-
-
3042846894
-
The structural genomics experimental pipeline: Insights from global target lists
-
O'Toole, N., M. Grabowski, Z. Otwinowski, W. Minor, and M. Cygler. 2004. The structural genomics experimental pipeline: insights from global target lists. Proteins. 56:201-210.
-
(2004)
Proteins
, vol.56
, pp. 201-210
-
-
O'Toole, N.1
Grabowski, M.2
Otwinowski, Z.3
Minor, W.4
Cygler, M.5
-
28
-
-
7444236378
-
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
-
Qian, B., A. R. Ortiz, and D. Baker. 2004. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc. Natl. Acad. Sci. USA. 101:15346-15351.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15346-15351
-
-
Qian, B.1
Ortiz, A.R.2
Baker, D.3
-
29
-
-
0030908273
-
Advances in comparative protein-structure modelling
-
Sanchez, R., and A. Sali. 1997. Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7:206-214.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 206-214
-
-
Sanchez, R.1
Sali, A.2
-
30
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi, J., T. L. Blundell, and K. Mizuguchi. 2001. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310:243-257.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
32
-
-
0000485973
-
The efficient generation of random orthogonal matrices with an application to condition estimation
-
Stewart, G. W. 1980. The efficient generation of random orthogonal matrices with an application to condition estimation. SIAM J. Humer. Anal. 17:403-409.
-
(1980)
SIAM J. Humer. Anal.
, vol.17
, pp. 403-409
-
-
Stewart, G.W.1
-
33
-
-
3242883858
-
On the potential of normal-mode analysis for solving difficult molecular-replacement problems
-
Suhre, K., and Y. H. Sanejouand. 2004. On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr. D Biol. Crystallogr. 60:796-799.
-
(2004)
Acta Crystallogr. D Biol. Crystallogr.
, vol.60
, pp. 796-799
-
-
Suhre, K.1
Sanejouand, Y.H.2
-
34
-
-
6344231648
-
Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
-
Temiz, N. A., E. Meirovitch, and I. Bahar. 2004. Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data. Proteins. 57:468-480.
-
(2004)
Proteins
, vol.57
, pp. 468-480
-
-
Temiz, N.A.1
Meirovitch, E.2
Bahar, I.3
-
35
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
36
-
-
0242330730
-
Assessment of homology-based predictions in CASP5
-
Tramontane, A., and V. Morea. 2003. Assessment of homology-based predictions in CASP5. Proteins. 53(Suppl. 6):352-368.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 352-368
-
-
Tramontane, A.1
Morea, V.2
-
37
-
-
0043238084
-
Dynamical properties of the MscL of Escherichia coli: A normal mode analysis
-
Valadie, H., J. J. Lacapcre, Y. H. Sanejouand, and C. Etchebest. 2003. Dynamical properties of the MscL of Escherichia coli: a normal mode analysis. J. Mol. Biol. 332:657-674.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 657-674
-
-
Valadie, H.1
Lacapcre, J.J.2
Sanejouand, Y.H.3
Etchebest, C.4
-
38
-
-
0030833135
-
Protein dynamics derived from clusters of crystal structures
-
van Aalten, D. M., D. A. Conn, B. L. de Groot, H. J. Berendsen, J. B. Findlay, and A. Amadei. 1997. Protein dynamics derived from clusters of crystal structures. Biophys. J. 73:2891-2896.
-
(1997)
Biophys. J.
, vol.73
, pp. 2891-2896
-
-
Aalten, D.M.1
Conn, D.A.2
De Groot, B.L.3
Berendsen, H.J.4
Findlay, J.B.5
Amadei, A.6
-
39
-
-
0141792364
-
Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T ↔ R2 transition
-
Xu, C., D. Tobi, and I. Bahar. 2003. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T ↔ R2 transition. J. Mol. Biol. 333:153-168.
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 153-168
-
-
Xu, C.1
Tobi, D.2
Bahar, I.3
|