-
1
-
-
0026776874
-
Computational complexity of a problem in molecular structure prediction
-
Ngo JT, Marks J. Computational complexity of a problem in molecular structure prediction. Protein Eng 1992;5:313-321.
-
(1992)
Protein Eng
, vol.5
, pp. 313-321
-
-
Ngo, J.T.1
Marks, J.2
-
2
-
-
0030626588
-
The Levinthal paradox: Yesterday and today
-
Karplus M. The Levinthal paradox: yesterday and today. Fold Des 1997;2:S69-S75.
-
(1997)
Fold des
, vol.2
-
-
Karplus, M.1
-
4
-
-
84986513586
-
Efficient algorithm for the reconstruction of a protein backbone from the α-carbon coordinates
-
Rey A, Skolnick J. Efficient algorithm for the reconstruction of a protein backbone from the α-carbon coordinates. J Comp Chem 1992;13:443-456.
-
(1992)
J Comp Chem
, vol.13
, pp. 443-456
-
-
Rey, A.1
Skolnick, J.2
-
5
-
-
0025978283
-
Database algorithm for generating protein backbone and side-chain coordinates from a Ca trace application to model building and detection of coordinate errors
-
Holm L, Sander C. Database algorithm for generating protein backbone and side-chain coordinates from a Ca trace application to model building and detection of coordinate errors. J Mol Biol 1991;218:183-194.
-
(1991)
J Mol Biol
, vol.218
, pp. 183-194
-
-
Holm, L.1
Sander, C.2
-
6
-
-
0025288651
-
The building of protein structures from α-carbon coordinates
-
Correa PE. The building of protein structures from α-carbon coordinates. Proteins 1990;7:366-377.
-
(1990)
Proteins
, vol.7
, pp. 366-377
-
-
Correa, P.E.1
-
7
-
-
0026439783
-
Application of a directed conformational search for generating 3-D coordinates for protein structures from α-carbon coordinates
-
Bassolino-Klimas D, Bruccoleri RE. Application of a directed conformational search for generating 3-D coordinates for protein structures from α-carbon coordinates. Proteins 1992;14:465-474.
-
(1992)
Proteins
, vol.14
, pp. 465-474
-
-
Bassolino-Klimas, D.1
Bruccoleri, R.E.2
-
8
-
-
0027299504
-
Towards protein folding by global energy optimization
-
Abagyan RA. Towards protein folding by global energy optimization. FEBS Lett 1993;325:17-22.
-
(1993)
FEBS Lett
, vol.325
, pp. 17-22
-
-
Abagyan, R.A.1
-
9
-
-
0027640931
-
Genetic algorithms: Principles of natural selection applied to computation
-
Forrest S. Genetic algorithms: principles of natural selection applied to computation. Science 1993;261:872-878.
-
(1993)
Science
, vol.261
, pp. 872-878
-
-
Forrest, S.1
-
10
-
-
0030851311
-
Cn3D: A new generation of three-dimensional molecular structure viewer
-
Hogue CWV. Cn3D: a new generation of three-dimensional molecular structure viewer. Trends Biochem Sci 1997;22:314-316.
-
(1997)
Trends Biochem Sci
, vol.22
, pp. 314-316
-
-
Hogue, C.W.V.1
-
11
-
-
0017411710
-
The Protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJ, et al. The Protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
-
12
-
-
84986432811
-
On searching neighbors in computer simulations of macromolecular systems
-
Van Gunsteren WV, Berendsen HJC, Colonna F, Perahia P, Hollenberg JP, Lellouch P. On searching neighbors in computer simulations of macromolecular systems. J Comp Chem 1984;5:272-279.
-
(1984)
J Comp Chem
, vol.5
, pp. 272-279
-
-
Van Gunsteren, W.V.1
Berendsen, H.J.C.2
Colonna, F.3
Perahia, P.4
Hollenberg, J.P.5
Lellouch, P.6
-
13
-
-
0002429974
-
A vectorized "nearest-neighbors" algorithm of order N using a monotonic Lagrangian grid
-
Boris J. A vectorized "nearest-neighbors" algorithm of order N using a monotonic Lagrangian grid. J Comput Phys 1986;66:1-20.
-
(1986)
J Comput Phys
, vol.66
, pp. 1-20
-
-
Boris, J.1
-
14
-
-
0002439750
-
An efficient program for many-body simulation
-
Appel AW. An efficient program for many-body simulation. SIAM J Sci Stat Comput 1985;6:85-103.
-
(1985)
SIAM J Sci Stat Comput
, vol.6
, pp. 85-103
-
-
Appel, A.W.1
-
15
-
-
0043023536
-
Efficient algorithms with neural network behavior
-
Omohundro SM. Efficient algorithms with neural network behavior. Complex Systems 1987;1:273-347.
-
(1987)
Complex Systems
, vol.1
, pp. 273-347
-
-
Omohundro, S.M.1
-
16
-
-
33846349887
-
A hierarchical O(N log N) force-calculation algorithm
-
Barnes J, Hut P. A hierarchical O(N log N) force-calculation algorithm. Nature 1986;324:446-449.
-
(1986)
Nature
, vol.324
, pp. 446-449
-
-
Barnes, J.1
Hut, P.2
-
17
-
-
84988106729
-
An algorithm for the representation and computation of supermolecular surfaces and volumes
-
Karfunkle HR, Eyraud V. An algorithm for the representation and computation of supermolecular surfaces and volumes. J Comput Chem 1989;10:628-634.
-
(1989)
J Comput Chem
, vol.10
, pp. 628-634
-
-
Karfunkle, H.R.1
Eyraud, V.2
-
18
-
-
0023165505
-
Hierarchical N-body methods
-
Hernquist L. Hierarchical N-body methods. Comput Phys Comm 1988;48:107-115.
-
(1988)
Comput Phys Comm
, vol.48
, pp. 107-115
-
-
Hernquist, L.1
-
19
-
-
0042839537
-
Computational structure of the N-body problem
-
Katzenelson J. Computational structure of the N-body problem. SIAM J Sci Stat Comput 1989;10:787-815.
-
(1989)
SIAM J Sci Stat Comput
, vol.10
, pp. 787-815
-
-
Katzenelson, J.1
-
21
-
-
0026305716
-
Protein folding. Effect of packing density on chain conformation
-
Gregoret LM, Cohen FE. Protein folding. Effect of packing density on chain conformation. J Mol Biol 1991;219:109-122.
-
(1991)
J Mol Biol
, vol.219
, pp. 109-122
-
-
Gregoret, L.M.1
Cohen, F.E.2
-
23
-
-
0033548058
-
Non-proline cis peptide bonds in proteins
-
Jabs A, Weiss MS, Hilgenfeld R. Non-proline cis peptide bonds in proteins. J Mol Biol 1999;286:291-304.
-
(1999)
J Mol Biol
, vol.286
, pp. 291-304
-
-
Jabs, A.1
Weiss, M.S.2
Hilgenfeld, R.3
-
24
-
-
0025299887
-
Occurrence and role of cis peptide bonds in protein structures
-
Stewart DE, Sarkar A, Wampler JE. Occurrence and role of cis peptide bonds in protein structures. J Mol Biol 1990;214:253-260.
-
(1990)
J Mol Biol
, vol.214
, pp. 253-260
-
-
Stewart, D.E.1
Sarkar, A.2
Wampler, J.E.3
-
25
-
-
0000164395
-
Crystallographic refinement by simulated annealing
-
Isaacs NW, Taylor MR, editors. Chester: Oxford University Press
-
Brunger AT. Crystallographic refinement by simulated annealing. In: Isaacs NW, Taylor MR, editors. Crystallographic computing 4. New techniques and new technologies. Chester: Oxford University Press; 1988. p 126-140.
-
(1988)
Crystallographic Computing 4. New Techniques and New Technologies
, pp. 126-140
-
-
Brunger, A.T.1
-
26
-
-
12944317826
-
Refinement techniques: Use of the FFT
-
Sayre D, editor. Oxford: Oxford University Press
-
Isaacs N. Refinement techniques: use of the FFT. In: Sayre D, editor. Computational crystallography. Oxford: Oxford University Press; 1982. p 398-408.
-
(1982)
Computational Crystallography
, pp. 398-408
-
-
Isaacs, N.1
-
27
-
-
79952608525
-
Accurate bond and angle parameters for X-ray protein structure refinement
-
Engh RA, Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr 1991;A47:392-400.
-
(1991)
Acta Crystallogr
, vol.A47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
29
-
-
0031933198
-
A new procedure for constructing peptides into a given Cα chain
-
Wang Y, Huq HI, de la Cruz, XF, Lee B. A new procedure for constructing peptides into a given Cα chain. Fold Des 1998;3:1-10.
-
(1998)
Fold des
, vol.3
, pp. 1-10
-
-
Wang, Y.1
Huq, H.I.2
De La Cruz, X.F.3
Lee, B.4
-
30
-
-
0026019108
-
Prediction of protein side-chain conformation by packing optimization
-
Lee C, Subbiah S. Prediction of protein side-chain conformation by packing optimization. J Mol Biol 1991;217:373-388.
-
(1991)
J Mol Biol
, vol.217
, pp. 373-388
-
-
Lee, C.1
Subbiah, S.2
-
31
-
-
0028223845
-
Predicting protein mutant energetics by self-consistent ensemble optimization
-
Lee C. Predicting protein mutant energetics by self-consistent ensemble optimization. J Mol Biol 1994;236:918-939.
-
(1994)
J Mol Biol
, vol.236
, pp. 918-939
-
-
Lee, C.1
-
32
-
-
0027160197
-
Backbone-dependent rotamer library for proteins. Application to side-chain prediction
-
Dunbrack RLJ, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol 1993;230:543-574.
-
(1993)
J Mol Biol
, vol.230
, pp. 543-574
-
-
Dunbrack, R.L.J.1
Karplus, M.2
-
33
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack RLJ, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
-
(1997)
Protein Sci
, vol.6
, pp. 1661-1681
-
-
Dunbrack, R.L.J.1
Cohen, F.E.2
-
34
-
-
1842692143
-
A general definition of ring puckering coordinates
-
Cremer D, Pople JA. A general definition of ring puckering coordinates. J Am Chem Soc 1975;97:1354-1358.
-
(1975)
J Am Chem Soc
, vol.97
, pp. 1354-1358
-
-
Cremer, D.1
Pople, J.A.2
-
36
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
37
-
-
0000050840
-
The configuration of random polypeptide chains. II. Theory
-
Brant DA, Flory PJ. The configuration of random polypeptide chains. II. Theory. J Amer Chem Soc 1965;87:2791-2800.
-
(1965)
J Amer Chem Soc
, vol.87
, pp. 2791-2800
-
-
Brant, D.A.1
Flory, P.J.2
-
38
-
-
0026633175
-
Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor
-
Amir D, Krausz S, Haas E. Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor. Proteins 1992;13:162-173.
-
(1992)
Proteins
, vol.13
, pp. 162-173
-
-
Amir, D.1
Krausz, S.2
Haas, E.3
-
39
-
-
0026992556
-
Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor
-
Gottfried DS, Haas E. Nonlocal interactions stabilize compact folding intermediates in reduced unfolded bovine pancreatic trypsin inhibitor. Biochemistry 1992;31:12353-12362.
-
(1992)
Biochemistry
, vol.31
, pp. 12353-12362
-
-
Gottfried, D.S.1
Haas, E.2
-
42
-
-
4244150856
-
Survival probability for kinetic self-avoiding walks
-
Pietronero L. Survival probability for kinetic self-avoiding walks. Phys Rev Lett 1985;55:2025-2027.
-
(1985)
Phys Rev Lett
, vol.55
, pp. 2025-2027
-
-
Pietronero, L.1
-
43
-
-
0017873321
-
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
-
Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978;120:97-120.
-
(1978)
J Mol Biol
, vol.120
, pp. 97-120
-
-
Garnier, J.1
Osguthorpe, D.J.2
Robson, B.3
-
44
-
-
0029884694
-
GOR method for predicting protein secondary structure from amino acid sequence
-
Garnier J, Gibrat J-F, Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 1996;266:540-553.
-
(1996)
Methods Enzymol
, vol.266
, pp. 540-553
-
-
Garnier, J.1
Gibrat, J.-F.2
Robson, B.3
|