-
2
-
-
33645747929
-
A constraint-based approach to fast and exact structure prediction in three-dimensional protein models
-
Backofen, R and Will, S (2006). "A constraint-based approach to fast and exact structure prediction in three-dimensional protein models." J Constraints 11, 5-30.
-
(2006)
J Constraints
, vol.11
, pp. 5-30
-
-
Backofen, R.1
Will, S.2
-
3
-
-
0031897962
-
Protein folding in the hydrophobichydrophilic (HP) model is NP-complete
-
Berger, B and Leighton, T (1998). "Protein folding in the hydrophobichydrophilic (HP) model is NP-complete." J. Comput. Biol. 5, 27-40.
-
(1998)
J. Comput. Biol.
, vol.5
, pp. 27-40
-
-
Berger, B.1
Leighton, T.2
-
4
-
-
35048820980
-
The protein sequence design problem in canonical model on 2D and 3D lattices
-
Springer, NewYork
-
Berman, P, DasGupta, B, Mubayi, D, Sloan, R, Turán, G and Zhang, Y (2004). "The protein sequence design problem in canonical model on 2D and 3D lattices." in Combinatorial Pattern Matching, Vol. 3109, pp. 244-253. Springer, NewYork.
-
(2004)
Combinatorial Pattern Matching
, vol.3109
, pp. 244-253
-
-
Berman, P.1
Dasgupta, B.2
Mubayi, D.3
Sloan, R.4
Turán, G.5
Zhang, Y.6
-
5
-
-
84857783719
-
-
BIU-home, Available as an opensource library from
-
BIU-home. (2007). BIU:bioinformatics utilities. Available as an opensource library from http://www.bioinf.uni-freiburg.de/sw/biu/.
-
BIU:Bioinformatics Utilities
-
-
-
6
-
-
0030709797
-
Chain growth algorithms for HP-type lattice proteins
-
Bornberg-Bauer, E (1997). "Chain growth algorithms for HP-type lattice proteins." in RECOMB'97, pp. 47-55.
-
(1997)
RECOMB'97
, pp. 47-55
-
-
Bornberg-Bauer, E.1
-
7
-
-
0025150383
-
Origins of structure in globular proteins
-
Chan, HS and Dill, KA (1990). "Origins of structure in globular proteins." Proc. Natl. Acad. Sci. U.S.A. 87, 6388-6392.
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 6388-6392
-
-
Chan, H.S.1
Dill, K.A.2
-
8
-
-
33846829658
-
Monte Carlo study of substrateinduced folding and refolding of lattice proteins
-
Coluzza, I and Frenkel, D (2007). "Monte Carlo study of substrateinduced folding and refolding of lattice proteins." Biophys. J. 92, 1150-1156.
-
(2007)
Biophys. J.
, vol.92
, pp. 1150-1156
-
-
Coluzza, I.1
Frenkel, D.2
-
9
-
-
84857783391
-
-
CPSP-home, Available as an open-source package from
-
CPSP-home. (2008). CPSP-tools: constraint-based protein structure prediction. Available as an open-source package from http://www.bioinf.uni-freiburg.de/sw/cpsp/.
-
(2008)
CPSP-tools: Constraint-based Protein Structure Prediction
-
-
-
10
-
-
0036469703
-
Lattice models of protein folding permitting disordered native states
-
Crippen, GM and Chhajer, M (2002). "Lattice models of protein folding permitting disordered native states." J. Chem. Phys. 116, 2261.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 2261
-
-
Crippen, G.M.1
Chhajer, M.2
-
11
-
-
34547830876
-
Cotranslational protein folding-fact or fiction?
-
Deane, CM, Dong, M, Huard, FP, Lance, BK, and Wood, GR (2007). "Cotranslational protein folding-fact or fiction?" Bioinformatics 23, i142-8.
-
(2007)
Bioinformatics
, vol.23
-
-
Deane, C.M.1
Dong, M.2
Huard, F.P.3
Lance, B.K.4
Wood, G.R.5
-
12
-
-
0028929556
-
Principles of protein folding-a perspective from simple exact models
-
Dill, KA, Bromberg, S, Yue, K, Fiebig, KM, Yee, DP, Thomas, PD, and Chan, HS (1995). "Principles of protein folding-a perspective from simple exact models." Protein Sci. 4, 561-602.
-
(1995)
Protein Sci
, vol.4
, pp. 561-602
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
Fiebig, K.M.4
Yee, D.P.5
Thomas, P.D.6
Chan, H.S.7
-
13
-
-
84857786875
-
-
ELL-home, Available as an opensource library from
-
ELL-home. (2007). ELL: energy landscape library. Available as an opensource library from http://www.bioinf.uni-freiburg.de/sw/ell/.
-
(2007)
ELL: Energy Landscape Library
-
-
-
14
-
-
0031468437
-
Cotranslational protein folding
-
Fedorov, AN and Baldwin, TO (1997). "Cotranslational protein folding." J. Biol. Chem. 272, 32715-32715.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 32715
-
-
Fedorov, A.N.1
Baldwin, T.O.2
-
15
-
-
43749099405
-
Beyond energy minimization: Approaches to the kinetic folding of RNA
-
Flamm, C and Hofacker, IL (2008). "Beyond energy minimization: approaches to the kinetic folding of RNA." Chemical Monthly 139, 447-457.
-
(2008)
Chemical Monthly
, vol.139
, pp. 447-457
-
-
Flamm, C.1
Hofacker, I.L.2
-
16
-
-
0034021259
-
RNA folding at elementary step resolution
-
Flamm, C, Fontana, W, Hofacker, IL, and Schuster, P (2000). "RNA folding at elementary step resolution." RNA 6, 325-328.
-
(2000)
RNA
, vol.6
, pp. 325-328
-
-
Flamm, C.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
17
-
-
0036340121
-
Barrier trees of degenerate landscapes
-
Flamm, C, Hofacker, IL, Stadler, PF, and Wolfinger, MT (2002). "Barrier trees of degenerate landscapes." Z. Phys. Chem. 216, 155-173.
-
(2002)
Z. Phys. Chem.
, vol.216
, pp. 155-173
-
-
Flamm, C.1
Hofacker, I.L.2
Stadler, P.F.3
Wolfinger, M.T.4
-
18
-
-
0028361309
-
Folding of nascent polypeptide chains in a high molecular mass assembly with molecular chaperones
-
Frydman, J, Nimmesgern, E, Ohtsuka, K, and Hartl, FU (1994). "Folding of nascent polypeptide chains in a high molecular mass assembly with molecular chaperones." Nature (London) 370, 111-117.
-
(1994)
Nature (London)
, vol.370
, pp. 111-117
-
-
Frydman, J.1
Nimmesgern, E.2
Ohtsuka, K.3
Hartl, F.U.4
-
21
-
-
33645003465
-
Structure-approximating inverse protein folding problem in the 2D HP model
-
Gupta, A, Manuch, J, and Stacho, L (2005). "Structure-approximating inverse protein folding problem in the 2D HP model." J. Comput. Biol. 12, 1328-1345.
-
(2005)
J. Comput. Biol.
, vol.12
, pp. 1328-1345
-
-
Gupta, A.1
Manuch, J.2
Stacho, L.3
-
22
-
-
0000629179
-
Diffusion in hierarchies
-
Hoffmann, KH and Sibani, P (1988). "Diffusion in hierarchies." Phys. Rev. A 38, 4261-4270.
-
(1988)
Phys. Rev. A
, vol.38
, pp. 4261-4270
-
-
Hoffmann, K.H.1
Sibani, P.2
-
23
-
-
33747884282
-
Modelling sequential protein folding under kinetic control
-
Huard, FP. E, Deane, CM, and Wood, GR (2006). "Modelling sequential protein folding under kinetic control." Bioinformatics 22, e203-210.
-
(2006)
Bioinformatics
, vol.22
-
-
Huard, F.P.E.1
Deane, C.M.2
Wood, G.R.3
-
24
-
-
0036345270
-
Enumerating designing sequences in the HP model
-
Irback, A and Troein, C (2002). "Enumerating designing sequences in the HP model." J. Biol. Phys. 28, 1-15.
-
(2002)
J. Biol. Phys.
, vol.28
, pp. 1-15
-
-
Irback, A.1
Troein, C.2
-
25
-
-
33846661178
-
A tale of two tails: Why are terminal residues of proteins exposed?
-
Jacob, E and Unger, R (2007). "A tale of two tails: why are terminal residues of proteins exposed?" Bioinformatics 23, 225-230.
-
(2007)
Bioinformatics
, vol.23
, pp. 225-230
-
-
Jacob, E.1
Unger, R.2
-
26
-
-
34547830871
-
Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: A lattice study
-
Jacob, E, Horovitz, A, and Unger, R (2007). "Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study." Bioinformatics 23, i240-i248.
-
(2007)
Bioinformatics
, vol.23
-
-
Jacob, E.1
Horovitz, A.2
Unger, R.3
-
27
-
-
49249086678
-
Funnels in energy landscapes
-
Klemm, K, Flamm, C, and Stadler, PF (2008). "Funnels in energy landscapes." Eur. Phys. J. B 63, 387-391.
-
(2008)
Eur. Phys. J. B
, vol.63
, pp. 387-391
-
-
Klemm, K.1
Flamm, C.2
Stadler, P.F.3
-
28
-
-
0035404969
-
Cotranslational protein folding
-
Kolb, VA (2001). "Cotranslational protein folding." Mol. Biol. (Moscow) 35, 682-690.
-
(2001)
Mol. Biol. (Moscow)
, vol.35
, pp. 682-690
-
-
Kolb, V.A.1
-
29
-
-
0034595692
-
Co-translational folding of an eukaryotic multidomain protein in a prokaryotic translation system
-
Kolb, VA, Makeyev, EV, and Spirin, AS (2000). "Co-translational folding of an eukaryotic multidomain protein in a prokaryotic translation system." J. Biol. Chem. 275, 16597-16601.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 16597-16601
-
-
Kolb, V.A.1
Makeyev, E.V.2
Spirin, A.S.3
-
30
-
-
84857781874
-
-
Lat Pack-home, Available as an open-source package from
-
Lat Pack-home. (2008). "LatPack: lattice protein folding package." Available as an open-source package from http://www.bioinf.uni-freiburg.de/Software/.
-
(2008)
LatPack: Lattice Protein Folding Package
-
-
-
31
-
-
0024750637
-
A lattice statistical mechanics model of the conformational and sequence spaces of proteins
-
Lau, KF and Dill, KA (1989). "A lattice statistical mechanics model of the conformational and sequence spaces of proteins." Macromolecules 22, 3986-3997.
-
(1989)
Macromolecules
, vol.22
, pp. 3986-3997
-
-
Lau, K.F.1
Dill, K.A.2
-
32
-
-
0038715327
-
A complete and effective move set for simplified protein folding
-
Lesh, N, Mitzenmacher, M, and Whitesides, S (2003). "A complete and effective move set for simplified protein folding." In Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'03), pp. 188-195.
-
(2003)
Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'03)
, pp. 188-195
-
-
Lesh, N.1
Mitzenmacher, M.2
Whitesides, S.3
-
33
-
-
0002006297
-
Are there pathways for protein folding?
-
Levinthal, C (1968). "Are there pathways for protein folding?" Extrait du Journal de Chimie Physique 65(1), 44-45.
-
(1968)
Extrait Du Journal De Chimie Physique
, vol.65
, Issue.1
, pp. 44-45
-
-
Levinthal, C.1
-
34
-
-
34250103739
-
Nonergodicity of local, lengthconserving Monte Carlo algorithms for the self-avoiding walk
-
Madras, N and Sokal, AD (1987). "Nonergodicity of local, lengthconserving Monte Carlo algorithms for the self-avoiding walk." J. Stat. Phys. 47, 573-595.
-
(1987)
J. Stat. Phys.
, vol.47
, pp. 573-595
-
-
Madras, N.1
Sokal, A.D.2
-
35
-
-
5944256461
-
The pivot algorithm: A highly efficient Monte Carlo method for the self-avoiding walk
-
Madras, N and Sokal, AD (1988). "The pivot algorithm: a highly efficient Monte Carlo method for the self-avoiding walk." J. Stat. Phys. 50, 109-186.
-
(1988)
J. Stat. Phys.
, vol.50
, pp. 109-186
-
-
Madras, N.1
Sokal, A.D.2
-
36
-
-
80051765253
-
The energy landscape library-a platform for generic algorithms
-
Mann, M, Will, S, and Backofen, R (2007). "The energy landscape library-a platform for generic algorithms." in Proc. of BIRD'07, Vol. 217, pp. 83-86.
-
(2007)
Proc. of BIRD'07
, vol.217
, pp. 83-86
-
-
Mann, M.1
Will, S.2
Backofen, R.3
-
37
-
-
44449128110
-
CPSP-tools-exact and complete algorithms for high-throughput 3D lattice protein studies
-
Mann, M, Will, S, and Backofen, R (2008). "CPSP-tools-exact and complete algorithms for high-throughput 3D lattice protein studies." BMC Bioinf. 9, 230.
-
(2008)
BMC Bioinf
, vol.9
, pp. 230
-
-
Mann, M.1
Will, S.2
Backofen, R.3
-
38
-
-
33751292555
-
Curvature of the energy landscape and folding of model proteins
-
Mazzoni, LN and Casetti, L (2006). "Curvature of the energy landscape and folding of model proteins." Phys. Rev. Lett. 97, 218104.
-
(2006)
Phys. Rev. Lett.
, vol.97
, pp. 218104
-
-
Mazzoni, L.N.1
Casetti, L.2
-
39
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa, S and Jernigan, RL (1996). "Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading." J. Mol. Biol. 256, 623-644.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
40
-
-
0033203533
-
Co-translational folding of an alphavirus capsid protein in the cytosol of living cells
-
Nicola, AV, Chen, W, and Helenius, A (1999). "Co-translational folding of an alphavirus capsid protein in the cytosol of living cells." Nat. Cell Biol. 1, 341-345.
-
(1999)
Nat. Cell Biol.
, vol.1
, pp. 341-345
-
-
Nicola, A.V.1
Chen, W.2
Helenius, A.3
-
41
-
-
0029063717
-
The complexity and accuracy of discrete state models of protein structure
-
Park, BH and Levitt, M (1995). "The complexity and accuracy of discrete state models of protein structure." J. Mol. Biol. 249, 493-507.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 493-507
-
-
Park, B.H.1
Levitt, M.2
-
44
-
-
0002698766
-
Modeling protein folding: The beauty and power of simplicity
-
Shakhnovich, EI (1996). "Modeling protein folding: the beauty and power of simplicity." Folding Des. 1, R50-54.
-
(1996)
Folding Des
, vol.1
, pp. 50-54
-
-
Shakhnovich, E.I.1
-
45
-
-
34548086584
-
Stochastic protein folding simulation in the d-dimensional HP-model
-
Springer, NewYork
-
Steinhöfel, K, Skaliotis, A, and Albrecht, AA (2007). "Stochastic protein folding simulation in the d-dimensional HP-model." in Proceedings of the 1st Conference on BioInformatics Research and Development, pp. 381-394, Springer, NewYork.
-
(2007)
Proceedings of the 1st Conference on BioInformatics Research and Development
, pp. 381-394
-
-
Steinhöfel, K.1
Skaliotis, A.2
Albrecht, A.A.3
-
46
-
-
36048965924
-
A replica exchange Monte Carlo algorithm for protein folding in the HP model
-
Thachuk, C, Shmygelska, A, and Hoos, HH (2007). "A replica exchange Monte Carlo algorithm for protein folding in the HP model." BMC Bioinf. 8, 342.
-
(2007)
BMC Bioinf
, vol.8
, pp. 342
-
-
Thachuk, C.1
Shmygelska, A.2
Hoos, H.H.3
-
47
-
-
0027690211
-
Finding the lowest free energy conformation of a protein is an NP-hard problem: Proof and implications
-
Unger, R and Moult, J (1993). "Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications." Bull. Math. Biol. 55, 1183-1198.
-
(1993)
Bull. Math. Biol.
, vol.55
, pp. 1183-1198
-
-
Unger, R.1
Moult, J.2
-
48
-
-
0042797442
-
-
Cambridge University Press, Cambridge
-
Wales, DJ (2004). Energy Landscapes, Cambridge University Press, Cambridge.
-
(2004)
Energy Landscapes
-
-
Wales, D.J.1
-
49
-
-
2442687677
-
Exact folding dynamics of RNA secondary structures
-
Wolfinger, MT, Flamm, WA S-S C, Hofacker, IL, and Stadler, PF (2004). "Exact folding dynamics of RNA secondary structures." J. Phys. A 37, 4731-4741.
-
(2004)
J. Phys. A
, vol.37
, pp. 4731-4741
-
-
Wolfinger, M.T.1
Flamm, W.A.S.-S.C.2
Hofacker, I.L.3
Stadler, P.F.4
-
50
-
-
33646878794
-
Exploring the lower part of discrete polymer model energy landscapes
-
Wolfinger, M, Will, S, Hofacker, I, Backofen, R, and Stadler, P (2006). "Exploring the lower part of discrete polymer model energy landscapes." Europhys. Lett. 74, 725-732.
-
(2006)
Europhys. Lett.
, vol.74
, pp. 725-732
-
-
Wolfinger, M.1
Will, S.2
Hofacker, I.3
Backofen, R.4
Stadler, P.5
-
51
-
-
0028924552
-
Navigating the folding routes
-
Wolynes, PG, Onuchic, JN, and Thirumalai, D (1995). "Navigating the folding routes." Science 267, 1619-1620.
-
(1995)
Science
, vol.267
, pp. 1619-1620
-
-
Wolynes, P.G.1
Onuchic, J.N.2
Thirumalai, D.3
|