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H TANS760101
D Statistical contact potential derived from 25 x-ray protein structures
R PMID:1004017
A Tanaka, S. and Scheraga, H.A.
T Medium- and long-range interaction parameters between amino acids
for predicting three-dimensional structures of proteins
J Macromolecules 9, 945-950 (1976)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H TANS760102
D Number of contacts between side chains derived from 25 x-ray protein structures
R PMID:1004017
A Tanaka, S. and Scheraga, H.A.
T Medium- and long-range interaction parameters between amino acids
for predicting three-dimensional structures of proteins
J Macromolecules 9, 945-950 (1976)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
36
20 14
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38 15 21 24 17 22 15 52 23 40 68 20 17 41 19 31 20 7
65 45 50 52 43 32 40 103 44 81 105 64 19 45 42 71 53 32 33
101 44 50 53 53 46 39 183 42 216 306 67 52 114 58 106 79 62 85 152
//
H ROBB790102
D Interaction energies derived from side chain contacts in the interiors of
known protein structures
R PMID:513136
A Robson, B. and Osguthorpe, D.J.
T Refined Models for Computer-Simulation of Protein Folding - Applications
to the Study of Conserved Secondary Structure and Flexible Hinge Points
During the Folding of Pancreatic Trypsin-Inhibitor
J J. Mol. Biol. 132, 19-51 (1979)
* (Glu is not available)
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//
H BRYS930101
D Distance-dependent statistical potential (only energies of contacts within
0-5 Angstrooms are included)
R PMID:8497488
A Bryant, S.H. and Lawrence, C.E.
T An Empirical Energy Function for Threading Protein-Sequence Through the
Folding Motif
J Proteins 16, 92-112 (1993)
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//
H THOP960101
D Mixed quasichemical and optimization-based protein contact potential
R PMID:8876187
A Thomas, P.D. and Dill, K.A.
T An iterative method for extracting energy-like quantities
from protein structures
J Proc. Natl. Acad. Sci. USA 93, 11628-11633 (1996)
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//
H MIRL960101
D Statistical potential derived by the maximization of the harmonic mean of Z
scores
R PMID:9000638
A Mirny, L.A. and Shakhnovich, E.I.
T How to derive a protein folding potential? A new approach
to an old problem
J J. Mol. Biol. 264, 1164-1179 (1996)
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//
H VENM980101
D Statistical potential derived by the maximization of the perceptron criterion
R
A Vendruscolo, M. and Domany E.
T Pairwise contact potentials are unsuitable for protein folding
J J. Chem. Phys. 109, 11101-11108 (1998)
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//
H BASU010101
D Optimization-based potential derived by the modified perceptron criterion
R PMID:11391771
A Bastolla, U., Farwer, J., Knapp, E.W. and Vendruscolo, M.
T How to guarantee optimal stability for most representative
structures in the protein data bank
J Proteins 44, 79-96 (2001)
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//
H MIYS850102
D Quasichemical energy of transfer of amino acids from water to the protein
environment
A Miyazawa, S. and Jernigan, R.L.
T Estimation of Effective Interresidue Contact Energies
from Protein Crystal-Structures-Quasi-Chemical Approximation
J Macromolecules 18, 534-552 (1985)
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//
H MIYS850103
D Quasichemical energy of interactions in an average buried environment
A Miyazawa, S. and Jernigan, R.L.
T Estimation of Effective Interresidue Contact Energies
from Protein Crystal-Structures-Quasi-Chemical Approximation
J Macromolecules 18, 534-552 (1985)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H MIYS960101
D Quasichemical energy of transfer of amino acids from water to the protein
environment
R PMID:8604144
A Miyazawa, S. and Jernigan, R.L.
T Residue-residue potentials with a favorable contact pair term
and an unfavorable high packing density term, for simulation
and threading
J J. Mol. Biol. 256, 623-644 (1996)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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-1.83 -1.55
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//
H MIYS960102
D Quasichemical energy of interactions in an average buried environment
R PMID:8604144
A Miyazawa, S. and Jernigan, R.L.
T Residue-residue potentials with a favorable contact pair term
and an unfavorable high packing density term, for simulation
and threading
J J. Mol. Biol. 256, 623-644 (1996)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.13
0.30 0.12
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0.30 -0.92 -0.35 0.06 0.54 -0.18 0.12
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//
H MIYS960103
D Number of contacts between side chains derived from 1168 x-ray protein
structures
R PMID:8604144
A Miyazawa, S. and Jernigan, R.L.
T Residue-residue potentials with a favorable contact pair term
and an unfavorable high packing density term, for simulation
and threading
J J. Mol. Biol. 256, 623-644 (1996)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
11789
5205 1558
6465 3325 2605
7836 8981 6075 2951
4306 1120 1549 1584 5003
5037 3062 3368 3550 1375 1253
5933 8570 4550 4001 1189 3096 1884
17079 5656 7319 8632 4168 4918 5248 10881
3600 1883 2053 3603 1209 1332 2800 3425 1224
16465 4065 3331 4318 3830 3772 4498 9071 2525 8432
24837 6653 5751 5729 5395 6091 6706 13533 4133 26396 21432
6019 1803 4260 9501 1200 3304 10234 6054 1554 4199 6531 1354
5014 1463 1410 1389 1247 1490 1827 3376 1273 5188 8218 1456 1125
10516 2956 2940 3217 2573 3056 3114 6523 2581 10183 17228 3098 4546 4778
6368 3036 3077 3483 1983 2779 2989 6827 2097 4600 7632 2665 1916 3930 1824
11447 4790 5920 8327 3012 3957 6343 12019 3073 6443 10084 5117 2205 5567 4843 5458
11323 4720 5790 7362 2475 4412 6172 11312 3071 7958 11387 4940 2595 5281 4806 9465 4387
3453 1588 1381 1444 1168 1057 1521 2946 1091 3101 4810 1367 1393 2498 2253 1889 1708 519
7942 4433 3792 5105 2045 3350 4601 7235 2441 6770 10806 4678 2765 5549 4653 5537 5102 1975 2491
21733 4867 4792 4606 4768 4541 5241 13584 3215 19830 32623 5437 5343 12746 6518 9059 9906 3723 7777 14091
//
H MIYS990106
D Quasichemical energy of transfer of amino acids from water to the protein
environment
R PMID:10336383
A Miyazawa, S. and Jernigan, R.L.
T Self-consistent estimation of inter-residue protein contact energies
based on an equilibrium mixture approximation of residues
J Proteins 34, 49-68 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.12
0.24 0.19
0.15 0.10 -0.06
0.27 -0.24 0.02 0.29
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0.22 0.09 0.06 0.24 -0.07 0.20
0.38 -0.22 0.12 0.44 0.20 0.27 0.46
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0.07 0.05 0.00 -0.10 -0.36 0.15 0.00 0.00 -0.40
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0.41 0.66 0.22 -0.01 0.33 0.28 -0.06 0.29 0.38 0.24 0.22 0.76
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0.10 0.16 0.09 0.10 -0.13 0.22 0.18 -0.01 0.04 0.03 -0.02 0.36 0.05 -0.12 0.20 0.05
0.04 0.11 0.04 0.11 -0.15 0.12 0.16 -0.04 -0.03 -0.15 -0.15 0.33 -0.11 -0.15 0.13 0.04 0.03
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//
H MIYS990107
D Quasichemical energy of interactions in an average buried environment
R PMID:10336383
A Miyazawa, S. and Jernigan, R.L.
T Self-consistent estimation of inter-residue protein contact energies
based on an equilibrium mixture approximation of residues
J Proteins 34, 49-68 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.08
0.18 0.03
0.07 -0.08 -0.26
0.10 -0.51 -0.27 -0.09
0.01 0.32 0.21 0.25 -0.55
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0.19 -0.51 -0.19 0.04 0.31 -0.09 0.04
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0.06 -0.02 -0.03 0.03 0.03 -0.09 0.05 -0.07 -0.08 0.12 0.09 0.06 0.01 0.03 -0.11
0.01 -0.03 -0.12 -0.20 0.08 -0.04 -0.14 -0.10 -0.05 0.20 0.19 -0.05 0.19 0.10 -0.02 -0.17
0.01 -0.02 -0.11 -0.13 0.12 -0.08 -0.10 -0.07 -0.06 0.08 0.12 -0.02 0.09 0.13 -0.03 -0.12 -0.07
0.02 -0.02 0.07 0.15 -0.07 0.10 0.06 0.04 -0.08 -0.05 -0.03 0.06 -0.21 -0.08 -0.21 0.15 0.20 -0.10
0.05 -0.10 0.02 -0.03 0.16 -0.06 -0.06 0.03 -0.05 0.02 0.00 -0.12 -0.08 -0.02 -0.13 0.04 0.09 0.01 0.01
-0.07 0.23 0.25 0.40 -0.04 0.16 0.28 0.10 0.19 -0.16 -0.19 0.22 -0.03 -0.11 0.07 0.16 0.11 -0.01 0.08 -0.19
//
H LIWA970101
D Modified version of the Miyazawa-Jernigan transfer energy
A Liwo, A., Oldziej, S., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga,
H.A.
T A united-residue force field for off-lattice protein-structure simulations:
1. Functional forms and parameters of long-range side-chain interaction
potentials from protein crystal data.
J J. Comp. Chem. 18, 849-873 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-3.28
-2.56 -2.03
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-3.93 -3.00 -3.02 -2.82 -4.53 -3.05 -2.84 -3.42 -3.44 -5.01 -4.85 -2.69 -4.59 -4.89 -3.39 -3.35 -3.58 -4.63 -4.04 -4.64
//
H KESO980101
D Quasichemical transfer energy derived from interfacial regions of
protein-protein complexes
R PMID:9865952
A Keskin, O., Bahar, I., Badretdinov, A.Y., Ptitsyn, O.B. and Jernigan, R.L.
T Empirical solvent-mediated potentials hold for both intra-molecular
and inter-molecular inter-residue interactions
J Protein Science 7, 2578-2586 (1998)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-3.51
-3.26 -3.98
-2.06 -2.67 -1.99
-2.74 -3.92 -2.50 -2.47
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-3.65 -4.13 -3.00 -3.15 -4.37 -4.71
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-3.96 -4.32 -3.14 -3.63 -4.71 -4.75 -3.62 -3.34 -3.78 -5.39 -5.67 -2.64 -5.01 -5.33 -2.92 -3.43 -3.33 -5.12 -4.58
-3.86 -3.70 -2.76 -3.28 -4.82 -4.29 -3.20 -2.77 -4.14 -5.31 -6.03 -2.19 -5.16 -5.33 -2.43 -2.95 -2.87 -4.70 -4.54 -4.86
//
H KESO980102
D Quasichemical energy in an average protein environment derived from interfacial
regions of protein-protein complexes
R PMID:9865952
A Keskin, O., Bahar, I., Badretdinov, A.Y., Ptitsyn, O.B. and Jernigan, R.L.
T Empirical solvent-mediated potentials hold for both intra-molecular
and inter-molecular inter-residue interactions
J Protein Science 7, 2578-2586 (1998)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.38
0.16 -0.26
0.31 -0.02 -0.40
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0.00 -0.12 1.46 0.06 -2.38
0.08 -0.11 -0.05 0.21 0.21 -0.38
0.20 -0.87 -0.30 0.17 0.72 0.03 -0.20
0.08 -0.10 -0.09 0.11 -0.26 -0.11 0.50 -0.27
0.01 0.35 -0.52 0.00 -0.64 -0.31 -0.10 0.01 0.38
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-0.09 0.21 0.23 0.41 -0.34 0.17 0.34 0.33 0.25 -0.50 -0.42
0.06 0.15 -0.44 -0.87 -0.50 0.00 -1.11 -0.17 -0.01 0.32 0.52 -0.22
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-0.11 0.35 0.22 0.11 -0.22 0.05 0.30 0.17 -0.23 -0.33 -0.48 0.40 -0.40 -0.27 0.16 0.25 0.27 0.20 0.03 -0.49
//
H MOOG990101
D Quasichemical potential derived from interfacial regions of protein-protein
complexes
R PMID:10328272
A Moont, G., Gabb, H.A. and Sternberg, M.J.E.
T Use of pair potentials across protein interfaces in screening predicted
docked complexes
J Proteins 35, 364-373 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.48
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0.08 0.37 0.04 0.02 0.00 0.22 0.00 0.10 0.00 0.43 0.25 0.06 0.00 0.34 0.35 0.05 0.03 0.00
0.15 0.42 0.26 0.25 0.25 0.26 0.08 0.07 0.47 0.34 0.27 0.26 0.47 0.43 0.24 0.12 0.15 0.59 0.09
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//
H BETM990101
D Modified version of the Miyazawa-Jernigan transfer energy
R PMID:10048329
A Betancourt,M.R. and Thirumalai,D.
T Pair potentials for protein folding: Choice of reference states
and sensitivity of predicted native states to variations
in the interaction schemes
J Protein Science 8, 361-369 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.20
0.27 0.13
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0.43 -0.75 -0.01 0.40 0.46 0.10 0.45
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-0.35 0.18 0.55 0.54 -0.48 0.14 0.38 0.21 0.19 -0.60
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0.20 0.50 -0.14 -0.69 0.35 -0.20 -0.87 0.12 0.26 0.21 0.16 0.38
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-0.33 0.08 0.29 0.48 -0.53 -0.04 0.34 0.11 -0.19 -0.65 -0.78 0.11 -0.89 -0.82
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//
H TOBD000101
D Optimization-derived potential obtained for small set of decoys
R PMID:10813832
A Tobi, D., Shafran, G., Linial, N. and Elber, R.
T On the design and analysis of protein folding potentials
J Proteins 40, 71-85 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.17
0.03 1.01
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//
H TOBD000102
D Optimization-derived potential obtained for large set of decoys
R PMID:10813832
A Tobi, D., Shafran, G., Linial, N. and Elber, R.
T On the design and analysis of protein folding potentials
J Proteins 40, 71-85 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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-0.16 0.65
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0.24 -0.14 -0.04 -1.41 -0.32 0.00 1.13 0.87 0.91 -1.90 -0.85 0.33 -0.30 0.58 -2.51 -0.77 0.32 -1.35
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//
H PARB960101
D Statistical contact potential derived by the quasichemical approximation
R PMID:8627632
A Park, B. and Levitt, M.
T Energy functions that discriminate X-ray and near-native folds
from well-constructed decoys
J J. Mol. Biol. 258, 367-392 (1996)
* (Glu is not available)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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0.2 -0.9
0.3 -0.8 -0.7
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0.0 -0.9 -0.7 -0.3 -0.2 -0.5
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-0.5 -0.5 -0.3 0.1 -0.8 -0.6 -0.3 NA -0.9 -1.4 -1.3 -0.1 -1.5
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0.0 -0.6 -0.4 -0.3 -0.3 -0.5 -0.3 NA -0.7 -0.6 -0.3 0.0 -0.6 -0.7 0.0 -0.2 -0.5
-0.8 -1.3 -0.8 -0.6 -1.3 -1.0 -0.8 NA -1.5 -1.8 -1.7 -0.8 -2.0 -2.0 -1.3 -0.6 -0.9 -2.2
-0.7 -1.4 -0.8 -1.0 -0.8 -1.1 -1.0 NA -1.5 -1.4 -1.4 -1.0 -1.5 -1.7 -1.0 -0.6 -0.8 -1.8 -1.6
-0.3 -0.5 0.0 0.4 -0.5 -0.4 0.0 NA -0.5 -1.2 -1.2 0.1 -1.0 -1.5 0.0 0.0 -0.3 -1.6 -1.2 -1.1
//
H PARB960102
D Modified version of the Miyazawa-Jernigan transfer energy
R PMID:8627632
A Park, B. and Levitt, M.
T Energy functions that discriminate X-ray and near-native folds
from well-constructed decoys
J J. Mol. Biol. 258, 367-392 (1996)
* (Glu is not available)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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-2.4 -2.9
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-2.3 -2.4 -2.7 -2.3 -2.8 -2.5 -1.8 NA -2.6 -3.0 -2.8 -1.8 -3.4 -3.1 -2.2
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-3.2 -3.1 -3.4 -3.2 -3.5 -3.1 -2.7 NA -3.2 -3.8 -3.3 -2.8 -3.8 -3.4 -2.8 -2.9 -3.5
-3.8 -3.5 -3.5 -3.2 -4.3 -3.3 -2.8 NA -3.6 -4.7 -4.4 -3.3 -4.8 -4.4 -3.7 -3.1 -3.7 -4.7
-3.7 -3.6 -3.5 -3.5 -3.8 -3.4 -3.0 NA -3.7 -4.4 -4.1 -3.5 -4.4 -4.1 -3.5 -3.1 -3.6 -4.3 -4.1
-4.1 -3.5 -3.5 -2.8 -4.3 -3.4 -2.8 NA -3.5 -5.0 -4.7 -3.1 -4.7 -4.6 -3.2 -3.1 -3.9 -4.8 -4.5 -5.1
//
H KOLA930101
D Statistical potential derived by the quasichemical approximation
A Kolinski, A., Godzik, A. and Skolnick, J.
T A general method for the prediction of the three dimensional structure
and folding pathway of globular proteins: Application to designed helical
proteins
J J. Chem. Phys. 98, 7420-7433 (1993)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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1.0 1.7 0.1 -0.6 1.6 0.4 -0.7 1.2 0.3 0.8 1.1 1.9
0.1 0.1 0.2 1.0 -1.8 0.2 0.0 0.4 -0.9 -0.7 -0.6 0.5 -1.1
-0.6 -0.4 0.2 0.4 -1.5 0.0 0.1 0.1 -1.0 -0.8 -0.9 0.3 -1.1 -1.5
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-0.1 0.0 -0.3 -0.9 -0.4 0.0 -0.2 0.0 -0.6 0.4 0.4 0.5 0.0 0.0 0.4 -0.6
-0.3 0.1 -0.3 -0.6 0.0 -0.2 -0.2 0.0 -0.6 0.0 0.3 0.6 0.2 0.0 0.3 -0.5 -0.3
-0.7 -0.9 -0.1 -0.2 -0.5 -0.2 0.1 -0.5 -1.2 -0.9 -0.8 0.1 -1.3 -1.3 -0.7 -0.1 0.0 -0.8
-0.5 -0.4 -0.5 -0.3 -0.1 -0.5 0.0 -0.4 -0.8 -0.5 -0.1 -0.2 -0.6 -0.5 -0.9 -0.1 -0.2 -0.5 -0.8
-0.6 0.3 0.2 0.7 -0.8 0.2 0.4 0.2 -0.2 -0.7 -0.6 0.9 -0.5 -0.8 0.1 0.3 0.2 -0.8 -0.3 -0.9
//
H GODA950101
D Quasichemical statistical potential derived from buried contacts
R PMID:8535247
A Godzik, A., Kolinski, A. and Skolnick, J.
T Are Proteins Ideal Mixtures of Amino-Acids-Analysis
of Energy Parameter Sets
J Protein Science 4, 2107-2117 (1995)
* (Glu is not available)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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0.3 -1.0 -0.5 -0.3 0.4 -0.3 -0.4
NA NA NA NA NA NA NA NA
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-0.1 0.3 0.4 0.5 0.2 0.2 0.5 NA 0.4 -0.1
-0.1 0.3 0.3 0.6 0.1 0.3 0.5 NA 0.4 -0.1 -0.2
0.3 0.3 -0.5 -0.9 0.4 -0.3 -0.8 NA 0.0 0.2 0.3 0.1
0.0 0.3 0.1 0.5 0.1 0.1 0.3 NA 0.2 0.0 0.0 0.2 -0.2
-0.1 0.2 0.1 0.3 0.1 0.1 0.3 NA 0.1 0.0 -0.1 0.1 -0.1 -0.2
0.0 -0.3 -0.3 0.0 -0.1 -0.4 -0.1 NA -0.1 0.2 0.1 0.1 0.0 -0.1 -0.3
0.1 -0.3 -0.4 -0.5 0.1 -0.3 -0.5 NA -0.3 0.4 0.4 -0.3 0.3 0.1 -0.3 -0.4
0.0 -0.1 -0.3 -0.3 0.0 -0.2 -0.2 NA -0.1 0.1 0.2 -0.1 0.1 0.1 -0.2 -0.2 0.0
0.0 -0.1 0.0 0.0 0.2 -0.1 0.0 NA 0.0 0.1 0.1 -0.1 -0.1 -0.1 -0.4 0.2 0.2 0.0
-0.1 -0.3 -0.2 -0.2 0.1 -0.2 -0.3 NA -0.1 0.1 0.0 -0.3 -0.1 0.0 -0.4 -0.1 0.0 0.1 -0.1
-0.1 0.4 0.3 0.6 0.0 0.2 0.4 NA 0.5 -0.1 -0.1 0.4 0.1 0.0 0.1 0.3 0.2 0.1 0.1 -0.2
//
H SKOJ970101
D Statistical potential derived by the quasichemical approximation
R PMID:9070450
A Skolnick, J., Jaroszewski, L., Kolinski, A. and Godzik, A.
T Derivation and testing of pair potentials for protein folding.
When is the quasichemical approximation correct?
J Protein Science 6, 676-688 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
0.8
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1.2 -0.4 0.5 0.9 0.9 0.8 1.2
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-0.3 -0.1 0.4 0.7 -0.4 0.2 0.6 0.4 -0.1 -1.3 -1.2
1.3 1.1 0.7 0.2 1.3 0.5 0.0 0.9 1.0 0.5 0.5 2.1
-0.3 0.2 0.3 0.6 -0.3 0.1 0.4 0.5 -0.4 -1.0 -1.0 0.6 -1.1
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0.9 0.2 0.7 0.7 0.6 0.6 0.6 0.8 0.0 0.3 0.4 0.9 0.4 0.1 0.6 0.6
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-0.4 -0.7 -0.2 -0.2 -0.1 -0.3 -0.2 0.1 -0.8 -1.0 -0.9 -0.2 -1.1 -1.0 -0.5 0.1 -0.2 -1.2 -0.8
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//
H SKOJ000101
D Statistical quasichemical potential with the partially composition-corrected
pair scale
R PMID:10651034
A Skolnick, J., Kolinski, A. and Ortiz, A.
T Derivation of protein-specific pair potentials based on weak sequence
fragment similarity
J Proteins 38, 3-16 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
1.0
0.4 -0.1
0.8 0.0 0.1
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0.9 0.3 0.4 0.3 0.4 0.2 0.4 0.9 0.1 0.4 0.4 0.7 0.3 0.1 0.6 0.5
0.6 0.0 0.2 0.1 0.1 0.1 0.2 0.6 0.0 -0.2 0.0 0.5 -0.1 -0.2 0.5 0.2 0.2
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//
H SKOJ000102
D Statistical quasichemical potential with the composition-corrected pair scale
R PMID:10651034
A Skolnick, J., Kolinski, A. and Ortiz, A.
T Derivation of protein-specific pair potentials based on weak sequence
fragment similarity
J Proteins 38, 3-16 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
0.8
0.3 -0.3
0.7 -0.2 -0.2
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0.8 0.4 0.2 -0.2 -0.3 0.0 -0.4 0.6 0.1 0.3 0.3 0.6
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0.7 0.0 0.3 0.6 -0.4 0.0 0.4 0.8 -0.2 0.0 0.1 0.5 -0.4 -0.3 0.3
0.8 0.2 0.2 0.2 -0.4 0.1 0.3 0.8 -0.2 0.3 0.4 0.5 -0.1 0.0 0.4 0.2
0.5 0.0 0.1 0.1 -0.5 0.0 0.1 0.6 -0.2 -0.2 0.0 0.4 -0.3 -0.3 0.3 0.2 0.0
-0.6 -0.9 -0.6 -0.4 -1.5 -0.9 -0.5 -0.2 -1.2 -1.2 -1.2 -0.5 -1.6 -1.4 -0.9 -0.5 -0.6 -1.7
-0.3 -0.7 -0.3 -0.2 -1.0 -0.4 -0.2 0.2 -0.9 -0.9 -0.9 -0.3 -1.0 -1.0 -0.6 0.0 -0.2 -1.3 -0.9
0.0 0.0 0.3 0.6 -0.7 0.1 0.4 0.7 -0.3 -1.0 -0.9 0.4 -0.8 -0.9 0.2 0.4 -0.1 -1.0 -0.7 -0.7
//
H BONM030101
D Quasichemical statistical potential for the antiparallel orientation of
interacting side groups
R PMID:15072433
A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
T Protein fragment reconstruction using various modeling techniques
J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.1
0.6 0.4
0.7 0.1 0.6
1.0 -0.2 0.8 1.8
-0.3 -0.7 0.2 0.6 -2.3
0.6 0.2 0.8 1.2 0.1 0.8
1.0 -0.1 1.2 2.1 0.7 1.6 2.3
0.1 0.7 0.3 0.5 -0.4 0.6 1.0 0.1
0.4 0.0 -0.2 -0.3 -1.2 -0.1 0.0 0.5 -0.9
-0.4 -0.4 0.7 0.9 -0.2 0.3 0.7 0.2 -0.8 -0.5
-0.4 -0.4 0.8 1.0 -0.4 0.3 0.7 0.3 -0.6 -0.4 -0.4
1.0 1.0 1.4 0.9 0.4 1.5 1.4 1.0 0.3 0.7 0.6 2.5
-0.2 -0.3 0.5 1.1 -0.4 0.3 1.1 0.2 -0.7 -0.3 -0.3 0.7 -0.7
-0.3 -0.5 -0.4 -0.1 -1.4 -0.4 -0.1 0.3 -0.8 -1.4 -1.4 -0.2 -1.4 -1.6
0.4 -0.1 0.6 1.0 -0.1 0.6 1.0 0.4 -0.6 0.4 0.4 1.3 0.3 -0.7 0.4
0.3 -0.2 0.5 0.7 -0.1 0.7 0.9 0.1 -0.6 0.4 0.3 1.3 0.6 -0.7 0.5 0.3
0.2 -0.1 0.5 0.9 -0.1 0.6 1.0 0.2 -0.6 0.3 0.3 1.2 0.5 -0.8 0.6 0.5 0.6
0.1 -0.5 -0.4 -0.2 -1.2 -0.4 -0.2 0.3 -0.9 -1.2 -1.1 0.0 -1.1 -1.2 -0.8 -0.5 -0.8 -1.4
0.0 -0.3 -0.3 -0.2 -1.2 -0.3 -0.1 0.4 -0.6 -1.1 -1.1 0.0 -0.9 -1.2 -0.8 -0.6 -0.6 -1.1 -0.9
-0.5 -0.3 0.7 1.0 -0.3 0.4 0.8 0.1 -0.7 -0.5 -0.4 0.7 -0.2 -1.3 0.3 0.3 0.3 -1.1 -1.0 -0.6
//
H BONM030102
D Quasichemical statistical potential for the intermediate orientation of
interacting side groups
R PMID:15072433
A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
T Protein fragment reconstruction using various modeling techniques
J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
0.1
0.5 -0.2
0.4 -0.3 0.1
0.6 -0.8 0.2 0.6
-0.2 -0.6 0.3 0.3 -1.7
0.4 -0.4 0.3 0.6 0.3 0.6
0.8 -0.7 0.6 1.1 0.8 0.7 1.2
0.4 0.4 0.2 0.5 -0.3 0.5 0.9 0.1
0.5 -0.4 -0.5 -0.6 -1.1 -0.2 -0.4 0.4 -1.0
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-0.2 -0.4 0.6 0.8 -0.4 0.4 0.8 0.3 -0.5 -0.3 -0.5
0.8 0.2 0.6 0.1 0.8 0.8 0.2 0.7 0.0 1.0 0.8 1.6
0.0 -0.4 0.6 0.9 -0.3 0.5 0.9 0.2 -0.6 -0.2 -0.3 1.0 -0.5
0.0 -0.4 -0.4 -0.2 -1.2 -0.3 -0.1 0.2 -0.6 -1.1 -1.2 -0.1 -1.2 -1.4
0.5 -0.4 0.6 0.8 0.1 0.5 0.7 0.5 -0.5 0.4 0.4 1.1 0.3 -0.6 0.5
0.3 -0.4 0.3 0.2 -0.1 0.3 0.5 0.1 -0.6 0.4 0.4 0.7 0.4 -0.6 0.5 0.1
0.2 -0.3 0.4 0.3 0.0 0.4 0.5 0.2 -0.5 0.4 0.4 0.8 0.3 -0.6 0.5 0.2 0.3
0.3 -0.6 -0.5 -0.5 -1.1 -0.5 -0.3 0.2 -0.8 -1.0 -1.0 -0.2 -1.0 -1.2 -0.8 -0.7 -0.6 -1.1
0.2 -0.5 -0.6 -0.5 -1.0 -0.4 -0.4 0.2 -0.7 -0.8 -0.9 -0.3 -1.0 -1.0 -0.8 -0.6 -0.5 -1.0 -0.8
-0.2 -0.3 0.7 0.8 -0.3 0.6 0.9 0.3 -0.4 -0.2 -0.4 1.0 -0.2 -1.0 0.3 0.4 0.3 -0.9 -0.7 -0.2
//
H BONM030103
D Quasichemical statistical potential for the parallel orientation of interacting
side groups
R PMID:15072433
A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
T Protein fragment reconstruction using various modeling techniques
J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.1
0.3 -0.8
0.1 -0.8 -0.6
0.1 -1.2 -0.6 -0.2
-0.5 -0.6 -0.1 0.2 -1.6
0.2 -1.0 -0.3 -0.3 0.0 -0.3
0.4 -1.4 -0.2 0.1 0.6 -0.2 0.2
0.3 0.3 0.1 0.2 -0.2 0.2 0.4 0.1
0.0 -0.9 -0.8 -1.0 -1.3 -0.9 -1.0 0.3 -1.5
-0.4 -0.6 0.2 0.4 -0.8 0.0 0.2 0.1 -0.7 -1.0
-0.4 -0.6 0.2 0.5 -0.9 -0.2 0.2 0.2 -0.8 -1.0 -1.2
0.4 -0.4 -0.2 -0.8 0.5 -0.3 -1.0 0.4 -0.6 0.2 0.3 0.3
-0.3 -0.6 0.2 0.4 -0.7 0.0 0.3 0.2 -0.9 -0.8 -0.9 0.3 -1.0
-0.2 -0.6 -0.6 -0.3 -1.5 -0.6 -0.4 0.1 -0.9 -1.4 -1.4 -0.2 -1.4 -1.5
0.4 -0.5 0.3 0.5 -0.1 0.3 0.4 0.4 -0.6 0.3 0.4 0.6 0.2 -0.6 0.8
-0.2 -0.8 -0.4 -0.5 -0.5 -0.2 -0.2 0.0 -0.9 0.0 0.0 -0.1 0.0 -0.8 0.3 -0.5
-0.1 -0.9 -0.4 -0.4 -0.4 -0.4 -0.4 0.0 -0.9 -0.3 -0.3 -0.2 -0.2 -0.8 0.2 -0.5 -0.5
0.2 -0.7 -0.8 -0.5 -1.3 -0.9 -0.6 0.1 -1.1 -1.2 -1.1 -0.5 -1.1 -1.4 -0.9 -0.8 -0.8 -1.6
-0.1 -1.0 -0.8 -0.7 -1.1 -0.8 -0.7 0.0 -1.2 -1.2 -1.1 -0.8 -1.1 -1.3 -0.8 -0.8 -0.8 -1.3 -1.1
-0.4 -0.6 0.1 0.4 -0.9 0.0 0.2 0.1 -0.9 -0.9 -1.0 0.1 -0.8 -1.4 0.2 -0.2 -0.3 -1.1 -1.1 -1.0
//
H BONM030104
D Distances between centers of interacting side chains in the antiparallel
orientation
R PMID:15072433
A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
T Protein fragment reconstruction using various modeling techniques
J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
4.7
5.5 6.5
5.0 5.5 5.4
4.9 5.6 5.3 5.4
5.0 5.9 5.7 5.2 4.4
5.0 6.1 5.3 5.3 5.5 5.8
5.2 5.7 5.3 5.5 5.7 5.4 6.1
4.6 6.7 5.1 4.5 5.5 5.1 4.5 3.9
5.2 5.7 5.4 5.2 5.4 5.2 5.5 4.5 5.3
5.2 5.9 5.3 5.7 5.2 5.4 5.6 5.5 5.9 5.8
5.2 5.8 5.7 5.5 5.5 5.8 5.8 5.9 5.7 5.6 5.7
5.2 6.5 5.3 5.3 5.3 5.7 5.3 5.9 5.2 5.8 5.4 5.7
5.0 5.8 5.2 6.1 5.3 4.9 5.9 4.7 5.0 5.7 5.4 5.8 5.9
5.1 5.7 5.8 5.6 5.4 5.7 5.8 5.4 5.5 6.0 5.8 5.5 5.8 6.2
5.2 5.7 5.3 5.2 5.9 5.7 5.5 5.6 5.5 5.7 5.6 5.9 5.4 5.5 4.9
4.7 5.6 5.2 5.2 5.1 5.4 5.1 4.5 5.3 5.3 5.2 4.9 5.5 5.4 5.4 4.9
5.2 5.9 5.3 5.5 5.6 5.6 5.4 5.9 5.5 5.6 5.6 5.3 5.5 5.7 5.4 4.8 5.4
5.8 6.0 5.7 6.6 5.3 5.5 6.3 5.8 5.5 6.2 6.3 5.6 6.1 6.2 5.4 5.8 6.1 6.4
5.5 6.0 5.7 5.7 6.1 5.6 5.8 4.3 5.7 6.0 5.8 5.6 6.3 5.9 5.8 5.8 5.9 6.5 6.3
4.9 5.6 5.4 5.5 5.4 5.6 5.3 5.2 5.4 5.6 5.6 5.7 5.5 5.6 5.8 5.1 5.6 6.3 5.9 5.5
//
H BONM030105
D Distances between centers of interacting side chains in the intermediate
orientation
R PMID:15072433
A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
T Protein fragment reconstruction using various modeling techniques
J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
4.7
5.5 6.6
5.2 6.1 5.6
5.0 5.6 5.2 5.5
5.3 5.6 5.7 5.4 4.3
5.4 6.0 5.9 5.5 5.4 5.4
5.0 5.9 5.6 5.9 5.1 5.7 6.1
4.7 6.3 5.6 4.7 5.3 5.9 5.6 4.5
5.2 5.9 5.5 5.8 5.9 6.2 5.7 5.4 6.0
5.5 6.1 5.7 5.6 5.5 5.7 5.9 5.1 5.9 6.2
5.5 6.1 5.9 5.6 5.7 5.9 5.5 4.9 5.8 6.1 6.2
5.2 6.3 5.7 5.6 6.2 5.8 5.8 4.7 5.6 5.9 5.8 6.1
5.3 6.3 6.3 5.9 5.8 5.6 5.7 5.8 5.9 5.9 6.2 6.5 5.9
5.5 6.1 6.1 5.9 5.8 6.1 5.9 6.0 6.0 6.2 6.2 5.5 6.2 6.3
5.3 6.1 5.5 5.2 5.7 5.4 5.3 4.0 5.5 5.9 5.8 5.9 5.8 5.8 5.3
4.7 5.4 5.1 4.7 5.3 5.3 5.2 4.4 5.4 5.4 5.6 5.5 5.2 5.6 5.2 5.0
5.1 6.0 5.5 5.3 5.5 5.3 5.2 5.5 5.6 5.8 5.8 5.7 5.9 6.1 5.5 5.2 5.4
5.9 5.9 6.5 6.0 6.1 6.2 6.2 5.2 6.0 6.3 6.3 5.7 6.5 6.5 5.8 5.7 6.5 7.5
5.6 6.3 5.9 6.2 6.1 6.7 6.1 4.8 6.2 6.2 6.1 5.7 6.1 6.4 5.6 5.9 6.1 6.9 6.5
5.4 6.0 5.6 5.6 5.7 5.4 5.4 4.6 5.6 6.0 6.0 5.9 5.9 6.0 5.7 5.4 5.7 6.3 6.0 5.8
//
H BONM030106
D Distances between centers of interacting side chains in the parallel
orientation
R PMID:15072433
A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
T Protein fragment reconstruction using various modeling techniques
J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
4.8
5.5 6.7
4.9 6.0 6.1
5.0 6.0 5.0 5.0
5.1 6.1 5.2 5.1 4.2
5.3 6.4 5.9 5.5 6.1 6.1
4.8 6.1 5.0 5.0 5.7 6.5 5.7
4.5 6.7 5.3 6.1 5.2 7.2 5.3 4.5
5.3 5.5 5.5 5.5 6.0 6.8 5.8 5.3 6.2
5.5 6.2 5.3 6.0 5.9 6.0 5.9 5.2 6.3 6.4
5.4 6.0 5.8 5.6 5.7 5.6 5.7 5.7 5.8 6.3 6.2
5.4 5.3 5.9 5.8 6.5 5.8 6.3 4.9 5.9 5.9 6.0 5.5
5.3 6.1 5.7 5.5 5.3 5.2 6.2 5.3 5.7 6.1 6.3 5.8 5.5
5.8 5.9 6.1 5.6 5.9 6.1 6.0 5.3 6.1 6.4 6.3 5.8 6.0 6.4
4.9 5.3 5.1 5.4 5.2 5.8 5.6 4.4 5.4 5.9 5.9 5.4 6.1 5.6 5.2
4.9 5.7 5.2 5.4 5.5 5.3 4.9 5.1 5.5 5.8 5.5 5.4 5.5 5.5 5.1 5.0
4.9 6.0 5.2 5.2 6.0 6.3 5.3 5.0 5.9 6.1 5.9 5.6 5.7 5.9 5.3 5.2 5.5
5.8 6.3 6.2 6.3 6.5 6.7 6.8 4.5 6.6 6.6 6.6 5.0 6.6 6.3 5.9 5.6 6.5 7.0
5.7 6.5 6.1 6.2 5.9 5.5 6.5 6.2 5.7 6.2 6.0 5.8 6.0 6.1 6.0 6.1 6.5 6.1 6.2
5.2 6.0 5.4 5.6 5.8 6.0 5.5 4.9 5.8 6.1 6.1 6.3 5.9 6.1 5.5 5.4 5.8 6.4 6.1 5.8
//
H MICC010101
D Optimization-derived potential
R PMID:11151013
A Micheletti, C., Seno, F., Banavar, J.R. and Maritan, A.
T Learning effective amino acid interactions through iterative
stochastic techniques
J Proteins 42, 422-431 (2001)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
0.001461
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0.003323 -0.006728 -0.001962
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0.005029 -0.001210 0.004502 -0.001466 0.001387 0.008438
-0.002376 -0.004586 -0.003154 0.002194 0.002791 -0.005234 0.006456
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0.000864 -0.001302 -0.000605 0.000585 -0.000196 -0.004168 -0.000453 -0.001538 -0.004529 -0.000782 -0.000748
0.001754 0.007273 0.006158 -0.000642 -0.006040 0.002349 -0.009604 -0.001308 0.002934 0.000855 0.002119 0.005109
-0.001496 -0.004676 0.018413 0.001491 0.014331 -0.002908 0.003231 0.002339 0.031785 -0.009283 -0.002531 -0.004667 0.031655
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//
H SIMK990101
D Distance-dependent statistical potential (contacts within 0-5 Angstrooms)
R PMID:10336385
A Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C. and Baker,
D.
T Improved recognition of native-like protein structures using
a combination of sequence-dependent and sequence-independent
features of proteins
J Proteins 34, 82-95 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H SIMK990102
D Distance-dependent statistical potential (contacts within 5-7.5 Angstrooms)
R PMID:11782533
A Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C. and Baker,
D.
T Improved recognition of native-like protein structures using
a combination of sequence-dependent and sequence-independent
features of proteins
J Proteins 34, 82-95 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H SIMK990103
D Distance-dependent statistical potential (contacts within 7.5-10 Angstrooms)
R PMID:11782533
A Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C. and Baker,
D.
T Improved recognition of native-like protein structures using
a combination of sequence-dependent and sequence-independent
features of proteins
J Proteins 34, 82-95 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H SIMK990104
D Distance-dependent statistical potential (contacts within 10-12 Angstrooms)
R PMID:11782533
A Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C. and Baker,
D.
T Improved recognition of native-like protein structures using
a combination of sequence-dependent and sequence-independent
features of proteins
J Proteins 34, 82-95 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H SIMK990105
D Distance-dependent statistical potential (contacts longer than 12 Angstrooms)
R PMID:11782533
A Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystroff, C. and Baker,
D.
T Improved recognition of native-like protein structures using
a combination of sequence-dependent and sequence-independent
features of proteins
J Proteins 34, 82-95 (1999)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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//
H ZHAC000101
D Environment-dependent residue contact energies (rows = helix, cols = helix)
R PMID:10706611
A Zhang, C. and Kim, S.H.
T Environment-dependent residue contact energies for proteins
J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-1.65
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//
H ZHAC000102
D Environment-dependent residue contact energies (rows = helix, cols = strand)
R PMID:10706611
A Zhang, C. and Kim, S.H.
T Environment-dependent residue contact energies for proteins
J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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-1.99 0.25 -0.20 1.00 -2.44 -0.12 0.88 -1.54 -0.05 -2.64 -2.33 0.75 -1.85 -2.46 -1.06 -0.59 -0.65 -1.82 -1.88 -2.45
-2.02 0.34 -0.04 0.13 -2.29 0.24 0.73 -1.27 -0.46 -2.53 -2.44 0.67 -1.80 -2.28 -1.29 -0.40 -0.34 -1.76 -1.66 -2.26
0.60 3.11 2.23 1.06 0.50 1.80 1.65 0.82 1.25 0.10 0.34 3.51 0.98 -0.21 1.15 2.09 1.30 -0.14 0.28 0.13
-1.54 -0.06 -0.63 1.76 -2.51 0.14 0.72 -1.74 0.07 -2.27 -2.22 1.27 -1.77 -1.87 0.34 -0.02 -0.21 -0.93 -1.54 -1.81
-2.12 0.33 -0.70 0.17 -2.30 -0.59 0.26 -1.60 -0.88 -2.53 -2.44 -0.42 -1.83 -2.68 -1.40 -0.82 -0.61 -1.63 -1.83 -2.25
0.63 2.43 -0.19 1.31 -1.63 1.46 1.91 0.08 1.11 -0.20 0.47 1.94 -0.34 0.15 0.57 0.00 1.15 0.06 0.26 -0.06
-0.41 0.88 1.02 1.04 -0.21 1.27 0.94 0.04 0.75 -0.48 -0.67 2.28 0.45 -0.92 0.75 0.50 0.96 0.22 -0.19 -0.54
-0.32 1.48 0.35 0.43 -1.44 0.38 1.36 -0.38 0.20 -1.14 -1.00 1.38 -0.35 -0.97 -0.05 -0.16 0.29 -0.53 -0.76 -0.73
-1.85 0.45 -0.03 0.80 -1.64 -0.23 0.11 -0.95 0.67 -1.58 -2.13 0.61 -1.75 -1.59 -1.07 -0.34 -0.40 -1.29 -1.27 -1.79
-0.88 -0.20 -0.29 0.14 -1.31 0.09 0.71 -0.56 -0.57 -1.66 -1.38 1.40 -1.60 -1.97 -0.73 -0.32 -0.37 -1.40 -0.96 -1.38
-1.74 0.85 0.24 0.72 -2.25 0.45 0.81 -1.29 -0.24 -2.46 -2.38 0.37 -1.21 -2.16 -1.00 -0.10 -0.57 -1.34 -1.52 -2.31
//
H ZHAC000103
D Environment-dependent residue contact energies (rows = helix, cols = coil)
R PMID:10706611
A Zhang, C. and Kim, S.H.
T Environment-dependent residue contact energies for proteins
J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
0.12 1.17 0.84 0.90 -0.81 1.16 1.44 0.10 0.69 -0.81 -0.78 1.16 -0.22 -0.67 0.61 0.47 0.36 -0.72 -0.37 -0.43
0.98 1.65 1.16 0.60 -0.21 1.26 1.12 1.09 1.16 -0.04 -0.09 2.37 0.47 -0.04 1.22 1.05 0.92 -0.09 0.06 0.32
0.69 1.16 1.16 1.22 -0.06 1.23 1.45 0.96 0.88 0.26 0.12 1.48 0.32 0.03 1.14 0.73 0.62 0.62 0.53 0.23
0.90 0.40 1.06 1.45 0.58 1.88 2.18 1.13 0.69 0.43 0.65 0.95 0.75 0.33 1.41 0.39 0.54 -0.10 0.12 0.77
-0.83 0.10 0.40 0.12 -2.65 -0.24 0.96 -0.26 -0.26 -1.61 -1.77 0.80 -1.02 -1.47 -0.31 -0.31 -0.49 -1.30 -0.98 -1.62
1.13 1.10 1.28 1.37 0.14 1.62 1.84 1.29 1.31 0.05 -0.05 1.50 0.41 0.20 1.14 0.86 0.62 0.45 0.31 0.48
1.33 0.91 1.33 1.60 0.31 1.60 1.93 1.62 1.01 0.33 0.38 1.12 0.82 0.55 1.54 0.78 0.54 0.23 0.52 0.86
-0.22 0.72 0.27 0.47 -0.95 0.42 1.39 -0.23 0.40 -0.48 -0.81 1.04 -0.62 -0.36 0.41 0.23 -0.04 -0.71 0.08 -0.35
0.47 0.81 0.95 0.51 -1.56 0.90 0.89 0.86 0.20 -0.43 -0.48 1.31 -0.63 -0.41 0.56 0.40 0.28 -0.20 -0.22 -0.21
-0.58 0.17 0.61 0.46 -1.17 0.24 0.80 0.04 -0.16 -1.64 -1.66 0.87 -0.89 -1.56 -0.27 0.02 -0.32 -1.40 -1.13 -1.36
-0.44 0.20 0.50 0.71 -1.56 0.11 0.82 0.28 -0.15 -1.67 -1.62 0.72 -0.96 -1.55 0.02 0.19 -0.09 -1.46 -0.95 -1.32
1.07 2.48 1.75 0.98 0.42 1.68 1.04 1.31 1.39 0.41 0.29 2.95 0.98 0.27 1.63 1.51 1.48 0.32 0.60 0.64
-0.22 0.65 0.76 0.88 -0.95 0.68 1.92 0.27 0.31 -1.32 -1.04 1.02 -0.57 -1.60 0.07 0.47 0.04 -1.29 -0.85 -0.82
-0.33 -0.06 0.42 0.42 -1.90 0.25 0.64 0.12 -0.01 -1.64 -1.50 0.58 -1.36 -1.77 -0.30 0.02 0.04 -1.41 -1.36 -1.34
0.78 1.30 1.31 1.27 -0.04 1.44 1.71 0.69 0.84 0.05 0.15 1.68 0.38 0.27 1.05 1.19 0.83 -0.24 0.23 0.12
0.46 1.07 1.04 0.73 -0.31 1.47 1.23 0.57 0.58 -0.11 -0.24 1.37 0.08 -0.34 0.76 0.51 0.48 -0.04 0.47 0.18
0.50 0.90 0.75 0.91 -0.26 1.03 1.25 0.55 0.55 -0.20 -0.26 1.42 0.50 -0.22 0.88 0.69 0.56 0.41 0.11 -0.15
-0.41 -0.06 -0.19 0.32 -0.79 -0.14 0.58 0.07 -0.62 -1.58 -1.16 0.18 -1.03 -1.33 -0.56 0.15 -0.19 -1.83 -0.67 -0.92
-0.22 -0.07 0.52 0.46 -0.87 0.38 0.59 0.40 -0.17 -1.29 -1.15 0.83 -0.98 -1.16 -0.16 0.34 -0.12 -0.79 -0.77 -0.78
-0.51 0.49 0.48 0.67 -1.40 0.66 0.63 -0.06 0.28 -1.25 -1.50 1.14 -0.93 -1.36 -0.04 0.10 -0.01 -1.11 -0.82 -1.14
//
H ZHAC000104
D Environment-dependent residue contact energies (rows = strand, cols = strand)
R PMID:10706611
A Zhang, C. and Kim, S.H.
T Environment-dependent residue contact energies for proteins
J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-2.52
-1.24 0.03
-1.22 -0.80 -0.48
-1.22 -1.51 -1.17 -0.07
-3.40 -0.78 -1.72 -1.34 -3.74
-1.17 -0.68 -0.74 -0.71 -1.97 -0.10
-0.77 -1.24 -0.67 -0.18 -0.83 -0.47 0.72
-2.84 -1.25 -1.69 -1.64 -3.17 -1.60 -1.07 -2.60
-1.69 -0.94 -0.67 -1.44 -2.31 -1.04 -1.17 -2.08 -1.69
-3.27 -1.41 -1.41 -1.28 -3.73 -1.45 -1.48 -2.93 -1.86 -3.5
-3.29 -1.18 -1.45 -1.26 -3.63 -1.38 -1.23 -2.98 -1.86 -3.7 -3.5
-0.70 0.28 -0.35 -1.00 -0.74 -0.42 -1.06 -0.83 -0.61 -1.3 -1.2 0.47
-2.63 -0.98 -1.32 -1.04 -3.48 -1.66 -0.64 -2.48 -1.55 -3.1 -3.1 -1.17 -1.95
-2.99 -1.44 -1.41 -1.43 -3.61 -1.59 -1.22 -3.01 -1.83 -3.5 -3.5 -0.92 -3.13 -3.10
-1.64 -0.84 -0.78 -0.27 -1.92 -0.58 0.38 -1.85 -0.81 -1.6 -1.9 -0.41 -1.43 -1.75 0.20
-1.74 -0.81 -1.16 -1.09 -2.23 -1.10 -0.85 -2.03 -1.53 -1.6 -1.8 -0.83 -1.72 -1.77 -0.48 -1.03
-1.87 -0.89 -0.90 -1.00 -2.39 -1.03 -1.17 -1.84 -1.29 -2.0 -1.8 -1.12 -1.40 -1.52 -0.72 -1.31 -1.29
-2.20 -1.39 -1.13 -1.00 -3.03 -1.72 -1.21 -2.58 -1.50 -2.9 -2.8 -1.55 -2.31 -2.81 -2.05 -1.50 -1.00 -1.6
-2.57 -1.57 -1.47 -1.50 -2.92 -1.31 -1.27 -2.69 -1.74 -2.9 -2.7 -1.42 -2.26 -2.73 -1.69 -1.61 -1.46 -2.0 -1.6
-3.07 -1.26 -1.33 -1.08 -3.33 -1.33 -1.07 -2.78 -1.70 -3.5 -3.5 -1.21 -2.96 -3.21 -1.53 -1.83 -1.82 -2.4 -2.4 -3.1
//
H ZHAC000105
D Environment-dependent residue contact energies (rows = strand, cols = coil)
R PMID:10706611
A Zhang, C. and Kim, S.H.
T Environment-dependent residue contact energies for proteins
J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
-0.57 0.47 0.30 0.62 -1.60 0.45 0.61 -0.24 0.07 -1.64 -1.63 0.62 -1.03 -1.55 -0.11 -0.10 -0.34 -1.44 -0.39 -1.55
0.23 0.79 0.76 0.39 -0.41 0.92 0.76 0.52 0.51 -0.30 0.13 1.58 0.88 -0.07 0.60 0.65 0.37 0.14 0.32 0.17
-0.28 0.74 0.57 0.87 -0.68 0.52 1.00 -0.07 0.32 -0.31 -0.08 0.87 0.29 -0.17 0.57 0.11 0.19 0.04 0.24 -0.23
0.15 -0.25 0.46 0.69 -0.46 0.41 1.34 0.56 -0.51 -0.23 0.27 0.59 0.60 -0.38 1.02 0.08 0.05 -0.48 0.02 0.34
-1.19 -0.46 0.21 0.51 -3.30 0.26 0.20 -1.03 -0.72 -1.55 -1.71 0.27 -1.24 -1.70 -0.50 -0.55 -0.97 -0.67 -1.26 -1.62
0.63 1.18 0.92 1.37 -0.30 0.93 1.27 0.56 0.91 -0.28 -0.11 0.98 0.15 -0.30 0.64 0.88 0.68 -0.44 0.66 0.15
0.97 0.89 1.37 1.89 0.30 1.25 2.34 0.98 0.58 0.20 0.50 0.67 1.23 0.58 1.26 0.95 1.06 0.04 0.87 0.48
-0.64 0.12 0.27 0.31 -1.37 0.38 0.98 -0.40 -0.12 -1.58 -1.40 0.78 -0.46 -1.38 -0.21 0.05 -0.26 -1.41 -0.61 -1.13
-0.02 0.75 0.68 0.14 -0.58 0.73 0.84 0.41 -0.64 -0.75 0.03 1.46 -0.16 -0.49 0.52 0.31 -0.11 -1.00 -0.58 0.03
-0.94 -0.14 0.31 0.26 -1.70 0.07 0.46 -0.37 -0.50 -1.88 -1.79 0.84 -0.99 -1.82 -0.47 -0.05 -0.54 -1.65 -1.09 -1.64
-0.76 0.32 0.43 0.25 -1.63 0.22 0.68 -0.17 -0.40 -1.84 -1.70 0.47 -1.06 -1.76 -0.39 0.09 -0.42 -1.81 -1.15 -1.64
1.02 1.99 1.18 0.59 0.08 1.10 0.60 0.61 0.95 0.24 0.34 2.69 0.97 -0.03 1.23 1.07 0.83 0.00 0.26 0.36
-0.16 0.83 0.47 0.92 -1.63 0.36 0.71 -0.20 0.90 -1.00 -1.12 1.55 -0.31 -1.35 -0.01 0.34 0.20 -1.70 -0.60 -0.79
-0.70 0.03 0.63 0.15 -1.26 0.29 0.35 -0.11 -0.36 -1.73 -1.55 0.71 -0.97 -1.55 -0.28 -0.09 -0.32 -1.23 -0.91 -1.30
0.17 0.50 0.60 0.67 -1.31 0.50 0.94 0.02 -0.45 -1.26 -0.91 1.08 0.83 -0.87 0.63 0.31 0.26 -0.50 -0.55 -0.79
-0.06 0.99 0.73 0.86 -0.89 0.85 0.67 0.08 0.06 -0.22 -0.29 0.94 -0.08 -0.41 0.67 0.33 0.13 -1.01 0.13 -0.24
0.26 0.93 0.70 0.87 -0.78 0.58 1.20 0.12 0.52 -0.30 -0.24 1.11 0.01 -0.08 0.65 0.47 0.41 -0.31 0.12 -0.32
-0.03 -0.11 0.27 0.66 -1.50 0.65 0.50 -0.12 -0.32 -1.13 -1.01 0.52 -1.08 -1.04 -0.32 -0.03 -0.10 -0.67 -0.73 -0.64
-0.44 0.20 0.20 0.20 -1.26 0.16 0.10 -0.21 -0.52 -1.26 -1.30 0.60 -0.76 -1.17 -0.42 0.05 -0.27 -1.20 -0.75 -0.84
-0.83 0.20 0.48 0.62 -1.44 0.17 0.73 -0.12 -0.26 -1.64 -1.59 0.52 -0.70 -1.55 -0.28 0.12 -0.17 -1.16 -0.85 -1.42
//
H ZHAC000106
D Environment-dependent residue contact energies (rows = coil, cols = coil)
R PMID:10706611
A Zhang, C. and Kim, S.H.
T Environment-dependent residue contact energies for proteins
J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
0.12
0.56 1.18
0.59 0.83 0.83
0.65 0.33 0.61 1.15
-0.74 -0.25 -0.07 -0.12 -2.42
0.70 0.94 0.87 0.96 -0.05 1.22
1.32 0.54 1.09 1.48 0.20 1.11 2.18
0.11 0.65 0.79 0.75 -0.56 0.73 1.16 0.35
0.35 0.47 0.91 0.29 -0.83 0.83 0.74 0.53 0.28
-0.45 0.05 0.40 0.47 -1.27 0.24 0.70 0.01 -0.21 -1.04
-0.25 0.26 0.37 0.57 -1.25 0.38 0.82 0.13 -0.03 -1.15 -1.04
1.06 1.65 1.11 0.58 0.76 1.29 0.93 1.08 1.23 0.48 0.78 2.23
0.29 0.58 0.68 0.75 -0.74 0.65 1.08 0.54 0.19 -0.52 -0.68 1.15 -0.12
-0.41 0.24 0.46 0.38 -1.44 0.39 0.55 0.09 -0.28 -1.09 -1.05 0.74 -0.60 -1.09
0.48 0.82 1.09 1.26 -0.23 1.09 1.25 0.74 0.59 0.14 0.10 1.59 0.54 -0.04 1.11
0.45 0.55 0.81 0.54 -0.47 0.75 0.87 0.61 0.46 0.09 0.01 1.24 0.56 0.17 0.94 0.87
0.30 0.80 0.54 0.51 -0.37 0.81 0.81 0.38 0.31 -0.28 -0.05 1.10 0.46 0.08 0.67 0.54 0.69
-0.28 -0.04 0.13 0.43 -0.63 -0.01 0.44 -0.17 -0.44 -1.28 -0.98 0.23 -0.50 -1.02 -0.33 0.14 -0.19 -0.46
-0.07 0.22 0.40 0.38 -0.58 0.09 0.47 0.28 -0.18 -0.74 -0.56 0.62 -0.26 -0.63 0.04 0.23 0.27 -0.87 -0.18
-0.18 0.43 0.54 0.59 -1.22 0.23 0.74 0.04 0.09 -0.90 -0.93 0.81 -0.31 -0.77 0.17 0.20 -0.10 -0.57 -0.38 -0.31
//
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