-
1
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJ, Prediction of protein-protein interactions by docking methods, Curr Opin Struct Biol 12(1):28-35, 2002.
-
(2002)
Curr Opin Struct Biol
, vol.12
, Issue.1
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.2
-
2
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R, Principles of docking: An overview of search algorithms and a guide to scoring functions, Proteins 47:409-443, 2002.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
3
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM, Principles of protein-protein interactions, Proc Natl Acad Sci USA 93(1):13-20, 1996.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, Issue.1
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
4
-
-
4444221565
-
UCSF ChimeraA visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE, UCSF ChimeraA visualization system for exploratory research and analysis, J Comput Chem 25(13): 1605-1612, 2004.
-
(2004)
J Comput Chem
, vol.25
, Issue.13
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
5
-
-
65449157423
-
-
The PyMOL molecular graphics system
-
DeLano WL, The PyMOL molecular graphics system, 2002.
-
(2002)
-
-
DeLano, W.L.1
-
6
-
-
0028929556
-
Principles of protein folding - A perspective from simple exact models
-
Dill KA, Principles of protein folding - A perspective from simple exact models, Protein Science 4(4):561-602, 1995.
-
(1995)
Protein Science
, vol.4
, Issue.4
, pp. 561-602
-
-
Dill, K.A.1
-
7
-
-
0027692037
-
Complexity of protein folding
-
Fraenkel AS, Complexity of protein folding, Bull Math Biol 55 (6):1199-1210, 1993.
-
(1993)
Bull Math Biol
, vol.55
, Issue.6
, pp. 1199-1210
-
-
Fraenkel, A.S.1
-
8
-
-
0031721615
-
On the complexity of protein folding
-
Crescenzi P, Goldman D, Papadimitriou CH, Piccolboni A, Yannakakis M, On the complexity of protein folding, J Comput Biol 5 (3):423-466, 1998.
-
(1998)
J Comput Biol
, vol.5
, Issue.3
, pp. 423-466
-
-
Crescenzi, P.1
Goldman, D.2
Papadimitriou, C.H.3
Piccolboni, A.4
Yannakakis, M.5
-
10
-
-
0030901866
-
General lattices and energy potentials
-
Robust proofs of NP-hardness for protein folding
-
Hart WE, Istrail S, Robust proofs of NP-hardness for protein folding: General lattices and energy potentials, J Comput Biol 4 (1):1-22, 1997.
-
(1997)
J Comput Biol
, vol.4
, Issue.1
, pp. 1-22
-
-
Hart, W.E.1
Istrail, S.2
-
11
-
-
0035703089
-
-
Bonneau R, Tsai J, Ruczinski I et al., Rosetta in CASP 4: Progress in ab-initio protein structure prediction, Proteins Structure Function and Genetics 45(s5):119-126, 2001.
-
Bonneau R, Tsai J, Ruczinski I et al., Rosetta in CASP 4: Progress in ab-initio protein structure prediction, Proteins Structure Function and Genetics 45(s5):119-126, 2001.
-
-
-
-
12
-
-
0036968925
-
De novo prediction of three-dimensional structures for major protein families
-
Bonneau R, Strauss CE, Rohl CA et al., De novo prediction of three-dimensional structures for major protein families, J Mol Biol 322(1):65-78, 2002.
-
(2002)
J Mol Biol
, vol.322
, Issue.1
, pp. 65-78
-
-
Bonneau, R.1
Strauss, C.E.2
Rohl, C.A.3
-
14
-
-
34249869832
-
Ab-initio modeling of small proteins by iterative TASSER simulations
-
Wu S, Skolnick J, Zhang Y, Ab-initio modeling of small proteins by iterative TASSER simulations, BMC Biology 5:17, 2007.
-
(2007)
BMC Biology
, vol.5
, pp. 17
-
-
Wu, S.1
Skolnick, J.2
Zhang, Y.3
-
15
-
-
33645923385
-
A supersecondary structure library and search algorithm for modeling loops in protein structures
-
Fernandez-Fuentes N, Oliva B, Fiser A, A supersecondary structure library and search algorithm for modeling loops in protein structures, Nucleic Acids Res 34(7):2085, 2006.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.7
, pp. 2085
-
-
Fernandez-Fuentes, N.1
Oliva, B.2
Fiser, A.3
-
16
-
-
33747854222
-
Developing a move-set for protein model refinement
-
Offman MN, Fitzjohn PW, Bates PA, Developing a move-set for protein model refinement, Bioinformatics 22(15):1838, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1838
-
-
Offman, M.N.1
Fitzjohn, P.W.2
Bates, P.A.3
-
17
-
-
0345043999
-
Searching in metric spaces
-
Chávez E, Navarro G, Baeza-Yates R, Marroquín JL, Searching in metric spaces, ACM Computing Surveys 33 (3):273-321, 2001.
-
(2001)
ACM Computing Surveys
, vol.33
, Issue.3
, pp. 273-321
-
-
Chávez, E.1
Navarro, G.2
Baeza-Yates, R.3
Marroquín, J.L.4
-
19
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang J, Cieplak P, Kollman PA, How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21 (12):1049-1074, 2000.
-
(2000)
J Comput Chem
, vol.21
, Issue.12
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
20
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI et al., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J Am Chem Soc 117(19):5179-5197, 1995.
-
(1995)
J Am Chem Soc
, vol.117
, Issue.19
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
-
21
-
-
84993661659
-
An efficient access method for similarity search in metric spaces
-
Ciaccia P, Patella M, Zezula P, M-tree: An efficient access method for similarity search in metric spaces, Proc 23rd Int Conf Very Large Data Bases, pp. 426-435, 1997.
-
(1997)
Proc 23rd Int Conf Very Large Data Bases
, pp. 426-435
-
-
Ciaccia, P.1
Patella, M.2
Zezula, P.3
M-tree4
-
22
-
-
0036509731
-
Fast indexing and visualization of metric data sets using slim-trees
-
Traina Jr C, Traina A, Faloutsos C, Seeger B, Fast indexing and visualization of metric data sets using slim-trees, IEEE Transactions on Knowledge and Data Engineering 14(2):244-260, 2002.
-
(2002)
IEEE Transactions on Knowledge and Data Engineering
, vol.14
, Issue.2
, pp. 244-260
-
-
Traina Jr, C.1
Traina, A.2
Faloutsos, C.3
Seeger, B.4
-
23
-
-
0025447750
-
The R*-tree: An efficient and robust access method for points and rectangles
-
Beckmann N, Kriegel HP, Schneider R, Seeger B, The R*-tree: An efficient and robust access method for points and rectangles, ACM SIGMOD Record 19(2):322-331, 1990.
-
(1990)
ACM SIGMOD Record
, vol.19
, Issue.2
, pp. 322-331
-
-
Beckmann, N.1
Kriegel, H.P.2
Schneider, R.3
Seeger, B.4
-
26
-
-
2542554197
-
Verification of protein structures: Side-chain planarity
-
Hooft RWW, Sander C, Vriend G, Verification of protein structures: Side-chain planarity, J Appl Crystallogr 29(6):714-716, 1996.
-
(1996)
J Appl Crystallogr
, vol.29
, Issue.6
, pp. 714-716
-
-
Hooft, R.W.W.1
Sander, C.2
Vriend, G.3
-
27
-
-
65449190324
-
-
http://swift.cmbi.kun.nl/whatif/select/.
-
-
-
-
28
-
-
0026661145
-
Selection of a representative set of structures from Brookhaven Protein Data Bank
-
Boberg J, Salakoski T, Vihinen M, Selection of a representative set of structures from Brookhaven Protein Data Bank, Proteins 14 (2):265-276, 1992.
-
(1992)
Proteins
, vol.14
, Issue.2
, pp. 265-276
-
-
Boberg, J.1
Salakoski, T.2
Vihinen, M.3
-
29
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm U, Sander C, Enlarged representative set of protein structures, Protein Science 3(3):522, 1994.
-
(1994)
Protein Science
, vol.3
, Issue.3
, pp. 522
-
-
Hobohm, U.1
Sander, C.2
-
30
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, The Protein Data Bank, Nucleic Acids Res 28(1):235-242, 2000.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
31
-
-
65449166974
-
-
http://www.rcsb.org/.
-
-
-
-
32
-
-
0029063717
-
The complexity and accuracy of discrete state models of protein structure
-
Park BH, Levitt M, The complexity and accuracy of discrete state models of protein structure, J Mol Biol 249:493-507, 1995.
-
(1995)
J Mol Biol
, vol.249
, pp. 493-507
-
-
Park, B.H.1
Levitt, M.2
-
33
-
-
0028429178
-
Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
-
Dunbrack RL, Karplus M, Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains, Nat Struct Biol 1(5):334-340, 1994.
-
(1994)
Nat Struct Biol
, vol.1
, Issue.5
, pp. 334-340
-
-
Dunbrack, R.L.1
Karplus, M.2
-
34
-
-
0036667731
-
Rotamer libraries in the 21st century
-
Dunbrack Jr RL, Rotamer libraries in the 21st century, Curr Opin Struct Biol 12(4):431-440, 2002.
-
(2002)
Curr Opin Struct Biol
, vol.12
, Issue.4
, pp. 431-440
-
-
Dunbrack Jr, R.L.1
-
35
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack Jr RL, Cohen FE, Bayesian statistical analysis of protein side-chain rotamer preferences, Protein Science 6 (8):1661-1681, 1997.
-
(1997)
Protein Science
, vol.6
, Issue.8
, pp. 1661-1681
-
-
Dunbrack Jr, R.L.1
Cohen, F.E.2
-
36
-
-
0027160197
-
Backbone-dependent rotamer library for proteins, Application to side-chain prediction
-
Dunbrack Jr RL, Karplus M, Backbone-dependent rotamer library for proteins, Application to side-chain prediction, J Mol Biol 230 (2):543-574, 1993.
-
(1993)
J Mol Biol
, vol.230
, Issue.2
, pp. 543-574
-
-
Dunbrack Jr, R.L.1
Karplus, M.2
|