-
1
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl MJ. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
2
-
-
0037197857
-
Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome
-
Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. (2002) Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci USA 99: 5993-5998.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5993-5998
-
-
Kihara, D.1
Zhang, Y.2
Lu, H.3
Kolinski, A.4
Skolnick, J.5
-
3
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM. (1992) A new approach to protein fold recognition. Nature 358: 86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
4
-
-
0026539511
-
Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native proteins
-
Casari G, Sippl MJ. (1992) Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native proteins. J Mol Biol 224: 725-732.
-
(1992)
J Mol Biol
, vol.224
, pp. 725-732
-
-
Casari, G.1
Sippl, M.J.2
-
5
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
6
-
-
0027650879
-
Boltzmann principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
-
Sippl MJ. (1993) Boltzmann principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aid Mol Des 7: 473-501.
-
(1993)
J Comput Aid Mol Des
, vol.7
, pp. 473-501
-
-
Sippl, M.J.1
-
7
-
-
33644842005
-
Improvement of statistical potentials and threading score functions using information maximization
-
Solis AD, Rackovsky S. (2006) Improvement of statistical potentials and threading score functions using information maximization. Proteins 62: 892-908.
-
(2006)
Proteins
, vol.62
, pp. 892-908
-
-
Solis, A.D.1
Rackovsky, S.2
-
8
-
-
33646808944
-
Accuracy of sequence allignment and fold assessment using reduced amino acid alphabets
-
Melo F, Marti-Renom M. (2004) Accuracy of sequence allignment and fold assessment using reduced amino acid alphabets. Proteins 63: 986-995.
-
(2004)
Proteins
, vol.63
, pp. 986-995
-
-
Melo, F.1
Marti-Renom, M.2
-
9
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo F, Sanchez R, Sali A. (2002) Statistical potentials for fold assessment. Protein Sci 11: 430-448.
-
(2002)
Protein Sci
, vol.11
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
10
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL. (1985) Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
11
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213: 859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
12
-
-
0032540222
-
Assessing protein structures with a non-local atomic interaction energy
-
Melo F, Feytmans E. (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277: 1141-1152.
-
(1998)
J Mol Biol
, vol.277
, pp. 1141-1152
-
-
Melo, F.1
Feytmans, E.2
-
13
-
-
0031582083
-
Novel knowledge-based mean force potential at atomic level
-
Melo F, Feytmans E. (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267: 207-222.
-
(1997)
J Mol Biol
, vol.267
, pp. 207-222
-
-
Melo, F.1
Feytmans, E.2
-
15
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
16
-
-
0027057526
-
A database of protein structure families with common folding motifs
-
Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G. (1992) A database of protein structure families with common folding motifs. Protein Sci 1:1691-1698.
-
(1992)
Protein Sci
, vol.1
, pp. 1691-1698
-
-
Holm, L.1
Ouzounis, C.2
Sander, C.3
Tuparev, G.4
Vriend, G.5
-
17
-
-
0034853119
-
DBAli: A database of protein structure alignments
-
Marti-Renom MA, Ilyin VA, Sali A. (2001) DBAli: a database of protein structure alignments. Bioinformatics 17: 746-747.
-
(2001)
Bioinformatics
, vol.17
, pp. 746-747
-
-
Marti-Renom, M.A.1
Ilyin, V.A.2
Sali, A.3
-
18
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J. (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
19
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J. (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44: 223-232.
-
(2001)
Proteins
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
20
-
-
34250886494
-
Non-bonded terms extrapolated from non-local knowledge based energy functions improve error detection in near native protein structure models
-
Ferrada E, Melo F. (2007) Non-bonded terms extrapolated from non-local knowledge based energy functions improve error detection in near native protein structure models. Protein Sci 16: 1410-1421.
-
(2007)
Protein Sci
, vol.16
, pp. 1410-1421
-
-
Ferrada, E.1
Melo, F.2
-
21
-
-
35348892593
-
A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
-
Ferrada E, Vergara IA, Melo F. (2007) A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations. Cell Biochem Biophys 49: 111-124.
-
(2007)
Cell Biochem Biophys
, vol.49
, pp. 111-124
-
-
Ferrada, E.1
Vergara, I.A.2
Melo, F.3
-
22
-
-
84969129749
-
Knowledge-based energy functions and effective atomic interactions
-
submitted
-
Ferrada E, Melo F. (2007) Knowledge-based energy functions and effective atomic interactions. Protein Sci, submitted.
-
(2007)
Protein Sci
-
-
Ferrada, E.1
Melo, F.2
-
23
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom MA, Stuart A, Fiser A, Sanchez R, Melo F, Sali A. (2000) Comparative protein structure modeling of genes and genomes. Ann Rev Biophys Biomol Struct 29: 291-325.
-
(2000)
Ann Rev Biophys Biomol Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
24
-
-
0033853177
-
Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction
-
Samudrala R, Levitt M. (2000) Decoys ‘R’ Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 9: 1399-1401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
25
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser A, Do RK, Sali A. (2000) Modeling of loops in protein structures. Protein Sci 9: 1753-1773.
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
26
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimizations and dynamic calculations
-
Brooks B, Bruccoleri R, Olafsonand B, et al. (1983) CHARMM: a program for macromolecular energy, minimizations and dynamic calculations. J Comput Chem 4: 187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafsonand, B.3
-
27
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Jr., Bashford D, Bellott M, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
-
28
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL. (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
29
-
-
84969156186
-
Evolutionary potentials: Structure specific potentials exploiting the evolutionary record of sequence homologs
-
Panjkovich A, Melo F, Marti-Renom MA. (2007) Evolutionary potentials:structure specific potentials exploiting the evolutionary record of sequence homologs. Protein Sci.
-
(2007)
Protein Sci
-
-
Panjkovich, A.1
Melo, F.2
Marti-Renom, M.A.3
-
30
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. (2001) Protein structure prediction and structural genomics. Science 294: 93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
31
-
-
35648999092
-
Fold assessment for comparative protein structure modeling
-
Melo F, Sali A. (2007) Fold assessment for comparative protein structure modeling. Protein Sci 16: 2142-2426.
-
(2007)
Protein Sci
, vol.16
, pp. 2142-2426
-
-
Melo, F.1
Sali, A.2
-
32
-
-
33644874394
-
MODBASE, a database of annotated comparative protein structure models, and associated resources
-
Pieper U, Eswar N, Braberg H, et al. (2006) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucl Acids Res 33: 291-295.
-
(2006)
Nucl Acids Res
, vol.33
, pp. 291-295
-
-
Pieper, U.1
Eswar, N.2
Braberg, H.3
-
33
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones DT. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287: 797-815.
-
(1999)
J Mol Biol
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
34
-
-
0038634975
-
Improvement of the GenTHREADER method for genomic fold recognition
-
McGuffin LJ, Jones DT. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.
-
(2003)
Bioinformatics
, vol.19
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
|