-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
2
-
-
0033954256
-
The protein data bank
-
Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
3
-
-
44449083478
-
Prediction of membrane-protein topology from first principles
-
Bernsel,A. et al. (2008) Prediction of membrane-protein topology from first principles. Proc. Natl Acad. Sci. USA, 105, 7177-7181.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 7177-7181
-
-
Bernsel, A.1
-
4
-
-
4444382786
-
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins
-
Beuming,T. and Weinstein,H. (2004) A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics, 20, 1822-1835.
-
(2004)
Bioinformatics
, vol.20
, pp. 1822-1835
-
-
Beuming, T.1
Weinstein, H.2
-
5
-
-
0002632234
-
An introduction to empirical bayes data analysis
-
Casella,G. (1985)An introduction to empirical bayes data analysis. Am. Stat., 39, 83-87.
-
(1985)
Am. Stat
, vol.39
, pp. 83-87
-
-
Casella, G.1
-
6
-
-
0348129526
-
The ASTRAL Compendium in 2004
-
Chandonia,J.M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Chandonia, J.M.1
-
8
-
-
0019872825
-
Helix to helix packing in proteins
-
Chothia,C. et al. (1981) Helix to helix packing in proteins. J. Mol. Biol., 145, 215-250.
-
(1981)
J. Mol. Biol
, vol.145
, pp. 215-250
-
-
Chothia, C.1
-
9
-
-
0037379072
-
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles
-
DeGrado,W.F. et al. (2003) How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci., 12, 647-665.
-
(2003)
Protein Sci
, vol.12
, pp. 647-665
-
-
DeGrado, W.F.1
-
10
-
-
3543089710
-
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
-
Dekker,J.P. et al. (2004) A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics, 20, 1565-1572.
-
(2004)
Bioinformatics
, vol.20
, pp. 1565-1572
-
-
Dekker, J.P.1
-
11
-
-
0036226583
-
Comparison of helix interactions in membrane and soluble alpha-bundle proteins
-
Eilers,M. et al. (2002) Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys. J., 82, 2720-2736.
-
(2002)
Biophys. J
, vol.82
, pp. 2720-2736
-
-
Eilers, M.1
-
12
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman,D. and Argos,P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
13
-
-
36949003878
-
Co-evolving residues in membrane proteins
-
Fuchs,A. et al. (2007) Co-evolving residues in membrane proteins. Bioinformatics, 23, 3312-3319.
-
(2007)
Bioinformatics
, vol.23
, pp. 3312-3319
-
-
Fuchs, A.1
-
14
-
-
30344453347
-
CASP6 assessment of contact prediction
-
Grana, et al. (2005) CASP6 assessment of contact prediction. Proteins, 61, 214-224.
-
(2005)
Proteins
, vol.61
, pp. 214-224
-
-
Grana1
-
15
-
-
10044249042
-
Helical packing patterns in membrane and soluble proteins
-
Gimpelev,M. et al. (2004) Helical packing patterns in membrane and soluble proteins. Biophys. J., 87, 4075-4086.
-
(2004)
Biophys. J
, vol.87
, pp. 4075-4086
-
-
Gimpelev, M.1
-
16
-
-
0033585083
-
The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction
-
Harrenga,A. and Michel,H. (1999) The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. J. Biol. Chem., 274, 33296-33299.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 33296-33299
-
-
Harrenga, A.1
Michel, H.2
-
17
-
-
36749082814
-
Assessment of intramolecular contact predictions for CASP7
-
Izarzugaza,J.M. et al. (2007) Assessment of intramolecular contact predictions for CASP7. Proteins, 69 (Suppl 8), 152-158.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 152-158
-
-
Izarzugaza, J.M.1
-
18
-
-
34047151404
-
Improving the accuracy of transmembrane protein topology prediction using evolutionary information
-
Jones,D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23, 538-544.
-
(2007)
Bioinformatics
, vol.23
, pp. 538-544
-
-
Jones, D.T.1
-
19
-
-
0036721218
-
Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
-
Kass,I. and Horovitz,A. (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48, 611-617.
-
(2002)
Proteins
, vol.48
, pp. 611-617
-
-
Kass, I.1
Horovitz, A.2
-
20
-
-
0032080907
-
Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils
-
Langosch,D. and Heringa,J. (1998) Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils. Proteins, 31, 150-159.
-
(1998)
Proteins
, vol.31
, pp. 150-159
-
-
Langosch, D.1
Heringa, J.2
-
21
-
-
0032125607
-
A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking
-
Li,A.J. and Nussinov,R. (1998) A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking. Proteins, 32, 111-127.
-
(1998)
Proteins
, vol.32
, pp. 111-127
-
-
Li, A.J.1
Nussinov, R.2
-
22
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li,W. and Godzick,A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzick, A.2
-
23
-
-
4143110064
-
Application of sparse NMR restraints to large-scale protein structure prediction
-
Li,W. et al. (2004) Application of sparse NMR restraints to large-scale protein structure prediction. Biophys. J., 87, 1241-1248.
-
(2004)
Biophys. J
, vol.87
, pp. 1241-1248
-
-
Li, W.1
-
24
-
-
39749179168
-
Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function
-
Lo,A. et al. (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J. Proteome Res., 7, 487-496.
-
(2008)
J. Proteome Res
, vol.7
, pp. 487-496
-
-
Lo, A.1
-
25
-
-
33644747742
-
Smoothing: Local regression techniques
-
Gentle,J, eds, Springer-Verlag, Heidelberg, pp
-
Loader,C. (2004) Smoothing: Local regression techniques. In Gentle,J. (eds) Handbook of Computational Statistics. Springer-Verlag, Heidelberg, pp. 540-560.
-
(2004)
Handbook of Computational Statistics
, pp. 540-560
-
-
Loader, C.1
-
26
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta., 405 442-451.
-
(1975)
Biochim. Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
27
-
-
64549140969
-
Exact inference in categorical data
-
Mehta,C.R. and Patel,N.R. (1997) Exact inference in categorical data. Biometrics, 53, 112-117.
-
(1997)
Biometrics
, vol.53
, pp. 112-117
-
-
Mehta, C.R.1
Patel, N.R.2
-
28
-
-
47049101751
-
Using inferred residue contacts to distinguish between correct and incorrect protein models
-
Miller,C.S. and Eisenberg,D. (2008) Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics, 24, 1575-1582.
-
(2008)
Bioinformatics
, vol.24
, pp. 1575-1582
-
-
Miller, C.S.1
Eisenberg, D.2
-
29
-
-
0004255908
-
-
WCB-McGraw-Hill, Boston, MA, pp
-
Mitchell,T.M. (1997) Machine Learning. WCB-McGraw-Hill, Boston, MA, pp. 96-97
-
(1997)
Machine Learning
, pp. 96-97
-
-
Mitchell, T.M.1
-
30
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea,O. and Valencia,A. (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des., 2, S25-S32.
-
(1997)
Fold Des
, vol.2
-
-
Olmea, O.1
Valencia, A.2
-
31
-
-
0032613288
-
Ab initio folding of proteins using restraints derived from evolutionary information
-
Ortiz,A.R. et al. (1999) Ab initio folding of proteins using restraints derived from evolutionary information. Proteins (Suppl 3), 177-185.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 177-185
-
-
Ortiz, A.R.1
-
32
-
-
46449120907
-
Predicting protein folding rates from geometric contact and amino acid sequence
-
Ouyang,Z. and Liang,J. (2008) Predicting protein folding rates from geometric contact and amino acid sequence. Protein Sci., 17, 1256-1263.
-
(2008)
Protein Sci
, vol.17
, pp. 1256-1263
-
-
Ouyang, Z.1
Liang, J.2
-
33
-
-
34948861813
-
Prediction of the burial status of transmembrane residues of helical membrane proteins
-
Park,Y. et al. (2007) Prediction of the burial status of transmembrane residues of helical membrane proteins. BMC Bioinformatics, 8, 302.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 302
-
-
Park, Y.1
-
34
-
-
0033790343
-
Helical membrane protein folding, stability, and evolution
-
Popot,J.L. and Engelman,D.M. (2000) Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem., 69, 881-922.
-
(2000)
Annu. Rev. Biochem
, vol.69
, pp. 881-922
-
-
Popot, J.L.1
Engelman, D.M.2
-
35
-
-
21444454088
-
PROFcon: Novel prediction of long-range contacts
-
Punta,M. and Rost,B. (2005) PROFcon: Novel prediction of long-range contacts. Bioinformatics, 21, 2960-2968.
-
(2005)
Bioinformatics
, vol.21
, pp. 2960-2968
-
-
Punta, M.1
Rost, B.2
-
36
-
-
0034711953
-
The GxxxG motif: A framework for transmembrane helix-helix association
-
Russ,W.P. and Engelman,D.M. (2000) The GxxxG motif: A framework for transmembrane helix-helix association. J. Mol. Biol., 296, 911-919.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 911-919
-
-
Russ, W.P.1
Engelman, D.M.2
-
37
-
-
34547131849
-
Specificity in transmembrane helix-helix interactions mediated by aromatic residues
-
Sal-Man,N. et al. (2007) Specificity in transmembrane helix-helix interactions mediated by aromatic residues. J. Biol. Chem., 282 19753-19761.
-
(2007)
J. Biol. Chem
, vol.282
, pp. 19753-19761
-
-
Sal-Man, N.1
-
38
-
-
0036700020
-
Quantifying the accessible surface area of protein residues in their local environment
-
Samanta,U. et al. (2002) Quantifying the accessible surface area of protein residues in their local environment. Protein Eng., 15, 659-667.
-
(2002)
Protein Eng
, vol.15
, pp. 659-667
-
-
Samanta, U.1
-
39
-
-
34548750953
-
Natively unstructured regions in proteins identified from contact predictions
-
Schlessinger,A. et al. (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics, 23, 2376-2384.
-
(2007)
Bioinformatics
, vol.23
, pp. 2376-2384
-
-
Schlessinger, A.1
-
40
-
-
36749031067
-
Contact prediction using mutual information and neural nets
-
Shackelford,G. and Karplus,K. (2007) Contact prediction using mutual information and neural nets. Proteins, 69 (Suppl 8), 159-164.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 159-164
-
-
Shackelford, G.1
Karplus, K.2
-
41
-
-
13444280419
-
PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank
-
Tusnady,G.E. et al. (2005) PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 33, D275-D278.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Tusnady, G.E.1
-
42
-
-
38549172064
-
TOPDB: Topology data bank of transmembrane proteins
-
Tusnady,G.E. et al. (2008) TOPDB: Topology data bank of transmembrane proteins. Nucleic Acids Res., 36, D234-D239.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Tusnady, G.E.1
-
43
-
-
33748791763
-
Helix-packing motifs in membrane proteins
-
Walters,R.F. and DeGrado,W.F. (2006) Helix-packing motifs in membrane proteins. Proc. Natl Acad. Sci. USA, 103, 13658-13663.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 13658-13663
-
-
Walters, R.F.1
DeGrado, W.F.2
-
44
-
-
34147130190
-
Computational design of peptides that target transmembrane helices
-
Yin,H. et al. (2007) Computational design of peptides that target transmembrane helices. Science, 315, 1817-1822.
-
(2007)
Science
, vol.315
, pp. 1817-1822
-
-
Yin, H.1
-
45
-
-
33646596891
-
Predicting the solvent accessibility of transmembrane residues from protein sequence
-
Yuan,Z. et al. (2006) Predicting the solvent accessibility of transmembrane residues from protein sequence. J. Proteome Res., 5, 1063-1070.
-
(2006)
J. Proteome Res
, vol.5
, pp. 1063-1070
-
-
Yuan, Z.1
-
46
-
-
0035956884
-
Polar residues drive association of polyleucine transmembrane helices
-
Zhou,F.X. et al. (2001) Polar residues drive association of polyleucine transmembrane helices. Proc. Natl Acad. Sci. USA, 98, 2250-2255.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 2250-2255
-
-
Zhou, F.X.1
|