-
1
-
-
0002725360
-
Chemical paleogenetics: Molecular "restoration studies" of extinct forms of life
-
Pauling, L., Zuckerkandl, E. Chemical paleogenetics: Molecular "restoration studies" of extinct forms of life. Acta Chem. Scand. 17:S9-S16, 1963.
-
(1963)
Acta Chem. Scand.
, vol.17
-
-
Pauling, L.1
Zuckerkandl, E.2
-
2
-
-
0028895702
-
Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily
-
Jermann, T.M., Optiz, J.G., Stackhouse, J., Benner, S.A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature (London) 374:57-59, 1995.
-
(1995)
Nature (London)
, vol.374
, pp. 57-59
-
-
Jermann, T.M.1
Optiz, J.G.2
Stackhouse, J.3
Benner, S.A.4
-
3
-
-
0029881442
-
Probabilistic reconstruction of ancestral protein sequences
-
Koshi, J.M., Goldstein, R.A. Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol. 42:413-420, 1996.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 413-420
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
4
-
-
0030931016
-
Mutation matrices and physical-chemical properties: Correlations and implications
-
Koshi, J.M., Goldstein, R.A. Mutation matrices and physical-chemical properties: Correlations and implications. Proteins 27:336-344, 1997.
-
(1997)
Proteins
, vol.27
, pp. 336-344
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
5
-
-
0003218786
-
A model of evolutionary change in proteins
-
Dayhoff, M.O., Eck, R.V. (eds.). Silver Spring, MD: National Biomedical Research Foundation
-
Dayhoff, M.O., Eck, R.V. A model of evolutionary change in proteins. In: "Atlas of Protein Sequence and Structure." Vol. 3. Dayhoff, M.O., Eck, R.V. (eds.). Silver Spring, MD: National Biomedical Research Foundation, 1968:33-41.
-
(1968)
Atlas of Protein Sequence and Structure
, vol.3
, pp. 33-41
-
-
Dayhoff, M.O.1
Eck, R.V.2
-
6
-
-
0025878149
-
Amino acid substitution matrices from an information theoretic perspective
-
Altschul, S.F. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219:555-565, 1991.
-
(1991)
J. Mol. Biol.
, vol.219
, pp. 555-565
-
-
Altschul, S.F.1
-
7
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S., Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89:10915-10919, 1992.
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
8
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D.T., Taylor, W.R., Thornton, J.M. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282, 1992.
-
(1992)
CABIOS
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
9
-
-
0025997601
-
Secondary structure-based profiles: Use of structure conserving scoring tables in searching protein sequence databases for structural similarities
-
Luthy, R., McLachlan, A.D., Eisenberg, D. Secondary structure-based profiles: Use of structure conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10:229-239, 1991.
-
(1991)
Proteins
, vol.10
, pp. 229-239
-
-
Luthy, R.1
McLachlan, A.D.2
Eisenberg, D.3
-
10
-
-
0015243774
-
Tests for comparing related amino-acid sequences
-
McLachlan, A.D. Tests for comparing related amino-acid sequences. J. Mol. Biol. 61:409-424, 1971.
-
(1971)
J. Mol. Biol.
, vol.61
, pp. 409-424
-
-
McLachlan, A.D.1
-
11
-
-
0027062943
-
Environment-specific amino-acid substitution tables: Tertiary templates and prediction of protein folds
-
Overington, J., Donnelly, D., Johnson, M.S. Šali, A., Blundell, T.L. Environment-specific amino-acid substitution tables: Tertiary templates and prediction of protein folds. Protein Sci. 1:216-226, 1992.
-
(1992)
Protein Sci.
, vol.1
, pp. 216-226
-
-
Overington, J.1
Donnelly, D.2
Johnson, M.S.3
Šali, A.4
Blundell, T.L.5
-
12
-
-
0024267619
-
Amino acid substitutions in structurally related proteins
-
Risler, J.L., Delorme, M.O., Delacroix, H., Henaut, A. Amino acid substitutions in structurally related proteins. J. Mol. Biol. 204:1019-1029, 1988.
-
(1988)
J. Mol. Biol.
, vol.204
, pp. 1019-1029
-
-
Risler, J.L.1
Delorme, M.O.2
Delacroix, H.3
Henaut, A.4
-
13
-
-
0021712450
-
Aligning amino-acid sequences: A comparison of commonly used methods
-
Feng, D.F., Johnson, M.S., Doolittle, R.F. Aligning amino-acid sequences: A comparison of commonly used methods. J. Mol. Evol. 21:112-125, 1985.
-
(1985)
J. Mol. Evol.
, vol.21
, pp. 112-125
-
-
Feng, D.F.1
Johnson, M.S.2
Doolittle, R.F.3
-
14
-
-
0013889249
-
An improved method of testing for evolutionary homology
-
Fitch, W.M. An improved method of testing for evolutionary homology. J. Mol. Biol. 16:9-16, 1966.
-
(1966)
J. Mol. Biol.
, vol.16
, pp. 9-16
-
-
Fitch, W.M.1
-
15
-
-
0016197604
-
Amino acid difference formula to help explain protein evolution
-
Grantham, R. Amino acid difference formula to help explain protein evolution. Science 185:862-864, 1974.
-
(1974)
Science
, vol.185
, pp. 862-864
-
-
Grantham, R.1
-
16
-
-
0018415510
-
Two types of amino acid substitutions in protein evolution
-
Miyata, T., Miyazawa, S., Yasunaga, T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:219-236, 1979.
-
(1979)
J. Mol. Evol.
, vol.12
, pp. 219-236
-
-
Miyata, T.1
Miyazawa, S.2
Yasunaga, T.3
-
17
-
-
0027191901
-
A new substitution matrix for protein sequence searches based on contact frequencies in protein structures
-
Miyazawa, S., Jernigan, R.L. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Eng. 6:267-278, 1993.
-
(1993)
Protein Eng.
, vol.6
, pp. 267-278
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
18
-
-
0023286275
-
New scoring matrix for amino acid residue exchange based on residue characteristic physical parameters
-
Rao, J.K.M. New scoring matrix for amino acid residue exchange based on residue characteristic physical parameters. Int. J. Pep. Prot. Res. 29:276-281, 1987.
-
(1987)
Int. J. Pep. Prot. Res.
, vol.29
, pp. 276-281
-
-
Rao, J.K.M.1
-
19
-
-
0028808763
-
Context-dependent optimal substitution matrices derived using Bayesian statistics and phylogenetic trees
-
Koshi, J.M., Goldstein, R.A. Context-dependent optimal substitution matrices derived using Bayesian statistics and phylogenetic trees. Protein Eng. 8:641-645, 1995.
-
(1995)
Protein Eng.
, vol.8
, pp. 641-645
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
20
-
-
0024046665
-
Cluster analysis of amino acid indices for prediction of protein structure and function
-
Nakai, K., Kidera, A., Kanehisa, M. Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2:93-100, 1988.
-
(1988)
Protein Eng.
, vol.2
, pp. 93-100
-
-
Nakai, K.1
Kidera, A.2
Kanehisa, M.3
-
21
-
-
0029922443
-
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
-
Tomii, K., Kanehisa, M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9:27-36, 1996.
-
(1996)
Protein Eng.
, vol.9
, pp. 27-36
-
-
Tomii, K.1
Kanehisa, M.2
-
22
-
-
0030902304
-
Amino acid substitutions preserve protein folding by conserving steric and hydrophobicity properties
-
Ladunga, I., Smith, R.F. Amino acid substitutions preserve protein folding by conserving steric and hydrophobicity properties. Protein Eng. 10:187-196, 1997.
-
(1997)
Protein Eng.
, vol.10
, pp. 187-196
-
-
Ladunga, I.1
Smith, R.F.2
-
23
-
-
0021931978
-
Statistical analysis of the physical properties of the 20 naturally occurring amino acids
-
Kidera, A., Konishi, Y., Oka, M., Ooi, T., Scheraga, H.A. Statistical analysis of the physical properties of the 20 naturally occurring amino acids. J. Protein Chem. 4:23-55, 1985.
-
(1985)
J. Protein Chem.
, vol.4
, pp. 23-55
-
-
Kidera, A.1
Konishi, Y.2
Oka, M.3
Ooi, T.4
Scheraga, H.A.5
-
24
-
-
0015244817
-
Empirical protein energy maps
-
Pohl, F.M. Empirical protein energy maps. Nat. New Biol. 234:227-279, 1971.
-
(1971)
Nat. New Biol.
, vol.234
, pp. 227-279
-
-
Pohl, F.M.1
-
25
-
-
0023645203
-
Interior and surface of monomeric proteins
-
Miller, S., Janin, J., Lesk, A.M., Chothia, C. Interior and surface of monomeric proteins. J. Mol. Biol. 196:641-656, 1987.
-
(1987)
J. Mol. Biol.
, vol.196
, pp. 641-656
-
-
Miller, S.1
Janin, J.2
Lesk, A.M.3
Chothia, C.4
-
26
-
-
0017619556
-
Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiment
-
Finkelstein, A.V., Ptitsyn, O.B., Kozitsyn, S.A. Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiment. Biopolymers 16:497-524, 1977.
-
(1977)
Biopolymers
, vol.16
, pp. 497-524
-
-
Finkelstein, A.V.1
Ptitsyn, O.B.2
Kozitsyn, S.A.3
-
27
-
-
0026709329
-
Alpha-helix stability in proteins
-
Serrano, L., Sancho, J., Hirshberg, M., Fersht, A.R. Alpha-helix stability in proteins. J. Mol. Biol. 227:544-559, 1992.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 544-559
-
-
Serrano, L.1
Sancho, J.2
Hirshberg, M.3
Fersht, A.R.4
-
28
-
-
0025890946
-
Influence of proline residues on protein conformation
-
MacArthur, M.W., Thornton, J.M. Influence of proline residues on protein conformation. J. Mol. Biol. 218:397-412, 1991.
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 397-412
-
-
MacArthur, M.W.1
Thornton, J.M.2
-
29
-
-
0026016378
-
The frequence of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions
-
Bryant, S.H., Lawrence, C.E. The frequence of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions. Proteins 9:108-119, 1991.
-
(1991)
Proteins
, vol.9
, pp. 108-119
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
30
-
-
0023051843
-
Internal cavities and buried waters in globular proteins
-
Rashin, A.A., Iofin, M., Honig, B. Internal cavities and buried waters in globular proteins. Biochem. 25:3619-3625, 1986.
-
(1986)
Biochem.
, vol.25
, pp. 3619-3625
-
-
Rashin, A.A.1
Iofin, M.2
Honig, B.3
-
31
-
-
0029184185
-
Boltzmann-like statistics of protein architectures
-
Finkelstein, A.V., Gutin, A.M., Badretdinov, A.Y. Boltzmann-like statistics of protein architectures. Subcell Biochem. 24:1-26, 1995.
-
(1995)
Subcell Biochem.
, vol.24
, pp. 1-26
-
-
Finkelstein, A.V.1
Gutin, A.M.2
Badretdinov, A.Y.3
-
32
-
-
3542999668
-
User's guide for MPSOL (version 4.0)
-
Stanford, CA: Department of Operations Research
-
Gill, P.E., Hammarling, S.J., Murray, W., Saunders, M.A., Wright, M.H. User's guide for MPSOL (version 4.0). Stanford, CA: Department of Operations Research, Stanford University Report SOL 86-2, 1986.
-
(1986)
Stanford University Report SOL 86-2
-
-
Gill, P.E.1
Hammarling, S.J.2
Murray, W.3
Saunders, M.A.4
Wright, M.H.5
-
33
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff, M.O. (ed.). Washington, D.C.: National Biomedical Research Foundation
-
Dayhoff, M.O., Schwartz, K.M., Orcutt, B.C. A model of evolutionary change in proteins. In: "Atlas of Protein Sequence and Structure." Vol. 5, suppl. 3. Dayhoff, M.O. (ed.). Washington, D.C.: National Biomedical Research Foundation, 1978:345.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, Issue.3 SUPPL.
, pp. 345
-
-
Dayhoff, M.O.1
Schwartz, K.M.2
Orcutt, B.C.3
-
34
-
-
0022591495
-
The classification of amino acid conservation
-
Taylor, W. The classification of amino acid conservation. J. Theor. Bio. 119:205-218, 1986.
-
(1986)
J. Theor. Bio.
, vol.119
, pp. 205-218
-
-
Taylor, W.1
-
35
-
-
0023375315
-
Profile analysis: Detection of distantly related proteins
-
Gribskov, M., McLachlan, A.D., Eisenberg, D. Profile analysis: Detection of distantly related proteins. Proc. Natl. Acad. Sci. U.S.A. 84:4355-4358, 1987.
-
(1987)
Proc. Natl. Acad. Sci. U.S.A.
, vol.84
, pp. 4355-4358
-
-
Gribskov, M.1
McLachlan, A.D.2
Eisenberg, D.3
-
36
-
-
0028181441
-
Hidden markov models in computational biology
-
Krogh, A., Brown, M., Mian, I.S., Sjölander, K., Haussler, D. Hidden markov models in computational biology. J. Mol. Biol. 235:1501-1531, 1994.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjölander, K.4
Haussler, D.5
-
37
-
-
0028091659
-
Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
-
Tatusov, R.L., Altschul, S.F., Koonin, E.V. Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. U.S.A. 91:12091-12095, 1994.
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 12091-12095
-
-
Tatusov, R.L.1
Altschul, S.F.2
Koonin, E.V.3
-
38
-
-
0027994453
-
Recognition of related proteins by iterative template refinement
-
Yi, T.M., Lander, E.S. Recognition of related proteins by iterative template refinement. Protein Sci. 3:1315-1328, 1994.
-
(1994)
Protein Sci.
, vol.3
, pp. 1315-1328
-
-
Yi, T.M.1
Lander, E.S.2
|