-
1
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
E. Alm and D. Baker. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. USA, 96(20): 11305-11310, 1999.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, Issue.20
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
2
-
-
0242438173
-
Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures
-
Special issue of Int. Conf. Comput. Molecular Biology (RECOMB) 2002
-
N. M. Amato, K. A. Dill, and G. Song. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. J. Comput. Biol., 10(3-4):239-256, 2003. Special issue of Int. Conf. Comput. Molecular Biology (RECOMB) 2002.
-
(2003)
J. Comput. Biol.
, vol.10
, Issue.3-4
, pp. 239-256
-
-
Amato, N.M.1
Dill, K.A.2
Song, G.3
-
3
-
-
0036100047
-
Using motion planning to study protein folding pathways
-
Special issue of Int. Conf. Comput. Molecular Biology (RECOMB) 2001
-
N. M. Amato and G. Song. Using motion planning to study protein folding pathways. J. Comput. Biol., 9(2):149-168, 2002. Special issue of Int. Conf. Comput. Molecular Biology (RECOMB) 2001.
-
(2002)
J. Comput. Biol.
, vol.9
, Issue.2
, pp. 149-168
-
-
Amato, N.M.1
Song, G.2
-
4
-
-
0036374348
-
Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion
-
M. Apaydin, D. Brutlag, C. Guestrin, D. Hsu, and J.-C. Latombe. Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pages 12-21, 2002.
-
(2002)
Proc. Int. Conf. Comput. Molecular Biology (RECOMB)
, pp. 12-21
-
-
Apaydin, M.1
Brutlag, D.2
Guestrin, C.3
Hsu, D.4
Latombe, J.-C.5
-
5
-
-
0034861208
-
Capturing molecular energy landscapes with probabilistic conformational roadmaps
-
M. Apaydin, A. Singh, D. Brutlag, and J.-C. Latombe. Capturing molecular energy landscapes with probabilistic conformational roadmaps. In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pages 932-939, 2001.
-
(2001)
Proc. IEEE Int. Conf. Robot. Autom. (ICRA)
, pp. 932-939
-
-
Singh, A.1
Brutlag, D.2
Latombe, J.-C.3
-
6
-
-
0034604105
-
A surprising simplicity to protein folding
-
D. Baker. A surprising simplicity to protein folding. Nature, 405:39-42, 2000.
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
7
-
-
0034868624
-
Ligand binding with OBPRM and haptic user input: Enhancing automatic motion planning with virtual touch
-
O. B. Bayazit, G. Song, and N. M. Amato. Ligand binding with OBPRM and haptic user input: Enhancing automatic motion planning with virtual touch. In Proc. IEEE Int. Conf. Robot. Autom. (ICRA), pages 954-959, 2001.
-
(2001)
Proc. IEEE Int. Conf. Robot. Autom. (ICRA)
, pp. 954-959
-
-
Bayazit, O.B.1
Song, G.2
Amato, N.M.3
-
8
-
-
33745777707
-
-
This work was also presented as a poster at RECOMB 2001.
-
RECOMB 2001
-
-
-
9
-
-
0033954256
-
The protein data bank
-
H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The protein data bank. Nucleic Acids Research, 28(1):235-242, 2000.
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.5
Weissig, H.6
Shindyalov, I.7
Bourne, P.8
-
10
-
-
0028826992
-
Automatic analysis of protein conformational changes by multiple linkage clustering
-
N. Boutonnet, M. Rooman, and S. Wodak. Automatic analysis of protein conformational changes by multiple linkage clustering. J. Mol Biol., 253:633-647, 1995.
-
(1995)
J. Mol Biol.
, vol.253
, pp. 633-647
-
-
Boutonnet, N.1
Rooman, M.2
Wodak, S.3
-
11
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
J. Bryngelson, J. Onuchic, N. Socci, and P. Wolynes. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Protein Struct. Funct. Genet, 21:167-195, 1995.
-
(1995)
Protein Struct. Funct. Genet
, vol.21
, pp. 167-195
-
-
Bryngelson, J.1
Onuchic, J.2
Socci, N.3
Wolynes, P.4
-
12
-
-
0000516026
-
Molecular dynamics and normal mode analysis of biomolecular rigidity
-
M. Thorpe and P. Duxbury, editors. Kluwer Academic/Plenum Publishers
-
D. Case. Molecular dynamics and normal mode analysis of biomolecular rigidity. In M. Thorpe and P. Duxbury, editors, Rigidity theory and applications, pages 329-344. Kluwer Academic/Plenum Publishers, 1999.
-
(1999)
Rigidity Theory and Applications
, pp. 329-344
-
-
Case, D.1
-
13
-
-
2342557155
-
Geometric algorithms for the conformational analysis of long protein loops
-
J. Cortes, T. Simeon, M. Remaud-Simeon, and V. Tran. Geometric algorithms for the conformational analysis of long protein loops. J. Computat. Chem., 25, 2004.
-
(2004)
J. Computat. Chem.
, pp. 25
-
-
Cortes, J.1
Simeon, T.2
Remaud-Simeon, M.3
Tran, V.4
-
14
-
-
0026761547
-
Folding protein α-carbon chains into compact forms by Monte Carlo methods
-
D. Covell. Folding protein α-carbon chains into compact forms by Monte Carlo methods. Proteins: Struct. Funct. Genet., 14(4):409-420, 1992.
-
(1992)
Proteins: Struct. Funct. Genet.
, vol.14
, Issue.4
, pp. 409-420
-
-
Covell, D.1
-
15
-
-
0037246863
-
Molmovdb: Analysis and visualization of conformational change and structural flexibility
-
N. Echols, D. Milburn, and M. Gerstein. Molmovdb: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res., 31:478-482, 2003.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 478-482
-
-
Echols, N.1
Milburn, D.2
Gerstein, M.3
-
16
-
-
0032530836
-
A database of macromolecular motions
-
M. Gerstein and W. Krebs. A database of macromolecular motions. Nucleic Acids Res., 26:4280-4290, 1998.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
18
-
-
0036888379
-
Identifying protein folding cores from the evolution of flexible regious during unfolding
-
B. M. Hespenheide, A. Rader, M. Thorpe, and L. A. Kuhn. Identifying protein folding cores from the evolution of flexible regious during unfolding. J. Mol. Gra. Model., 21:195-207, 2002.
-
(2002)
J. Mol. Gra. Model.
, vol.21
, pp. 195-207
-
-
Hespenheide, B.M.1
Rader, A.2
Thorpe, M.3
Kuhn, L.A.4
-
19
-
-
0032493601
-
Generic rigidity in three-dimensional bond-bending networks
-
D. Jacobs. Generic rigidity in three-dimensional bond-bending networks. J. Phys. A: Math. Gen., 31:6653-6668, 1998.
-
(1998)
J. Phys. A: Math. Gen.
, vol.31
, pp. 6653-6668
-
-
Jacobs, D.1
-
20
-
-
0000785338
-
Generic rigidity percolation: The pebble game
-
D. Jacobs and M. Thorpe. Generic rigidity percolation: The pebble game. Phys. Rev. Lett., 75(22):4051-4054, 1995.
-
(1995)
Phys. Rev. Lett.
, vol.75
, Issue.22
, pp. 4051-4054
-
-
Jacobs, D.1
Thorpe, M.2
-
21
-
-
0035427398
-
Protein flexiblility predictions using graph theory
-
D. J. Jacobs, A. Rader, L. A. Kuhn, and M. Thorpe. Protein flexiblility predictions using graph theory. Proteins Struct. Funct. Genet., 44:150-165, 2001.
-
(2001)
Proteins Struct. Funct. Genet.
, vol.44
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.2
Kuhn, L.A.3
Thorpe, M.4
-
22
-
-
0020655246
-
Structural domains in proteins and their role in the dynamics of protein function
-
J. Janin and S. Wodak. Structural domains in proteins and their role in the dynamics of protein function. Prog. Biophys. Mol. Biol., 42:21-78, 1983.
-
(1983)
Prog. Biophys. Mol. Biol.
, vol.42
, pp. 21-78
-
-
Janin, J.1
Wodak, S.2
-
23
-
-
0021918946
-
Prediction of chain flexibility in proteins
-
P. Karplus and G. Schulz. Prediction of chain flexibility in proteins. Naturwissencschaften, 72:212-213, 1985.
-
(1985)
Naturwissencschaften
, vol.72
, pp. 212-213
-
-
Karplus, P.1
Schulz, G.2
-
24
-
-
0030212126
-
Probabilistic roadmaps for path planning in high-dimensional configuration spaces
-
August
-
L. E. Kavraki, P. Svestka, J. C. Latombe, and M. H. Overmars. Probabilistic roadmaps for path planning in high-dimensional configuration spaces. IEEE Trans. Robot. Automat., 12(4):566-580, August 1996.
-
(1996)
IEEE Trans. Robot. Automat.
, vol.12
, Issue.4
, pp. 566-580
-
-
Kavraki, L.E.1
Svestka, P.2
Latombe, J.C.3
Overmars, M.H.4
-
25
-
-
0034029144
-
Proteins with similar architecture exhibit similar large-scale dynamic behavior
-
O. Keskin, R. Jernigan, and I. Bahar. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J., 78:2093-2106, 2000.
-
(2000)
Biophys. J.
, vol.78
, pp. 2093-2106
-
-
Keskin, O.1
Jernigan, R.2
Bahar, I.3
-
26
-
-
0034685619
-
A breakdown of symmetry in the folding transition state of protein 1
-
D. E. Kim, C. Fisher, and D. Baker. A breakdown of symmetry in the folding transition state of protein 1. J. Mol. Biol., 298:971-984, 2000.
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 971-984
-
-
Kim, D.E.1
Fisher, C.2
Baker, D.3
-
27
-
-
0028203492
-
Monte Carlo simulations of protein folding
-
A. Kolinski and J. Skolnick. Monte Carlo simulations of protein folding. Proteins Struct. Fund. Genet, 18(3):338-352, 1994.
-
(1994)
Proteins Struct. Fund. Genet
, vol.18
, Issue.3
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
28
-
-
0037115811
-
Free energy disconnectivity graphs: Application to peptide models
-
S. V. Krivov and M. Karplus. Free energy disconnectivity graphs: Application to peptide models. J. Chem. Phys, 114(23):10894-10903, 2002.
-
(2002)
J. Chem. Phys
, vol.114
, Issue.23
, pp. 10894-10903
-
-
Krivov, S.V.1
Karplus, M.2
-
29
-
-
2942536134
-
Sampling protein conformations and pathways
-
M. Lei, M. I. Zavodszky, L. A. Kuhn, and M. F. Thorpe. Sampling protein conformations and pathways. J. Comput. Chem., 25:1133-1148, 2004.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1133-1148
-
-
Lei, M.1
Zavodszky, M.I.2
Kuhn, L.A.3
Thorpe, M.F.4
-
30
-
-
0021095856
-
Protein folding by restrained energy minimization and molecular dynamics
-
M. Levitt. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol., 170:723-764, 1983.
-
(1983)
J. Mol. Biol.
, vol.170
, pp. 723-764
-
-
Levitt, M.1
-
31
-
-
0016610491
-
Computer simulation of protein folding
-
M. Levitt and A. Warshel. Computer simulation of protein folding. Nature, 253:694-698, 1975.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
32
-
-
0344603844
-
The hydrogen exchange core and protein folding
-
R. Li and C. Woodward. The hydrogen exchange core and protein folding. Protein Sci., 8(8):1571-1591, 1999.
-
(1999)
Protein Sci.
, vol.8
, Issue.8
, pp. 1571-1591
-
-
Li, R.1
Woodward, C.2
-
33
-
-
0032555216
-
The allosteric mechanism of the chaperonin groel: A dynamic analysis
-
J. Ma and M. Karplus. The allosteric mechanism of the chaperonin groel: a dynamic analysis. Proc. Natl. Acad. Sci. USA, 95:8502-8507, 1998.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 8502-8507
-
-
Ma, J.1
Karplus, M.2
-
34
-
-
0030939896
-
A new method for modeling large-scale rearrangements of protein domains
-
V. Maiorov and R. Abagyan. A new method for modeling large-scale rearrangements of protein domains. Proteins, 27:410-424, 1997.
-
(1997)
Proteins
, vol.27
, pp. 410-424
-
-
Maiorov, V.1
Abagyan, R.2
-
35
-
-
0033871567
-
Critical role of β-hairpin formation in protein g folding
-
E. L. McCallister, E. Aim, and D. Baker. Critical role of β-hairpin formation in protein g folding. Nat. Struct. Biol., 7(8):669-673, 2000.
-
(2000)
Nat. Struct. Biol.
, vol.7
, Issue.8
, pp. 669-673
-
-
McCallister, E.L.1
Aim, E.2
Baker, D.3
-
36
-
-
0032568537
-
A statistical mechanical model for β-hairpin kinetics
-
V. Muñoz, E. R. Henry, J. Hoferichter, and W. A. Eaton. A statistical mechanical model for β-hairpin kinetics. Proc. Natl. Acad. Sci. USA, 95:5872-5879, 1998.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 5872-5879
-
-
Muñoz, V.1
Henry, E.R.2
Hoferichter, J.3
Eaton, W.A.4
-
37
-
-
0034964196
-
Computer-based redesign of a protein folding pathway
-
S. Nauli, B. Kuhlman, and D. Baker. Computer-based redesign of a protein folding pathway. Nature Struct. Biol., 8(7):602-605, 2001.
-
(2001)
Nature Struct. Biol.
, vol.8
, Issue.7
, pp. 602-605
-
-
Nauli, S.1
Kuhlman, B.2
Baker, D.3
-
38
-
-
0029159748
-
Rigid domains in proteins: An algorithmic approach to their identification
-
W. Nichols, G. Rose, L. T. Eyck, and B. Zimm. Rigid domains in proteins: an algorithmic approach to their identification. Proteins, 23:38-48, 1995.
-
(1995)
Proteins
, vol.23
, pp. 38-48
-
-
Nichols, W.1
Rose, G.2
Eyck, L.T.3
Zimm, B.4
-
40
-
-
0037133552
-
Protein unfolding: Rigidity lost
-
A. Rader, B. M. Hespenheide, L. A. Kuhn, and M. Thorpe. Protein unfolding: Rigidity lost. Proc. Natl. Acad. Sci. USA, 99(6).-3540-3545, 2002.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, Issue.6
, pp. 3540-3545
-
-
Rader, A.1
Hespenheide, B.M.2
Kuhn, L.A.3
Thorpe, M.4
-
42
-
-
33745771854
-
-
Ph.D. dissertation, Dept. of Computer Science, Texas A&M University, December
-
G. Song. A Motion Planning Approach to Protein Folding. Ph.D. dissertation, Dept. of Computer Science, Texas A&M University, December 2004.
-
(2004)
A Motion Planning Approach to Protein Folding
-
-
Song, G.1
-
43
-
-
0042629768
-
A path planning-based study of protein folding with a case study of hairpin formation in protein G and L
-
G. Song, S. Thomas, K. Dill, J. Scholtz, and N. Amato. A path planning-based study of protein folding with a case study of hairpin formation in protein G and L. In Proc. Pacific Symposium of Biocomputing (PSB), pages 240-251, 2003.
-
(2003)
Proc. Pacific Symposium of Biocomputing (PSB)
, pp. 240-251
-
-
Song, G.1
Thomas, S.2
Dill, K.3
Scholtz, J.4
Amato, N.5
-
45
-
-
0028841399
-
A simple protein folding algorithm using a binary code and secondary structure constraints
-
S. Sun, P. D. Thomas, and K. A. Dill. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng., 8(8):769-778, 1995.
-
(1995)
Protein Eng.
, vol.8
, Issue.8
, pp. 769-778
-
-
Sun, S.1
Thomas, P.D.2
Dill, K.A.3
-
46
-
-
2442595997
-
Using motion planning to study rna folding kinetics
-
X. Tang, B. Kirkpatrick, S. Thomas, G. Song, and N. M. Amato. Using motion planning to study rna folding kinetics. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pages 252-261, 2004.
-
(2004)
Proc. Int. Conf. Comput. Molecular Biology (RECOMB)
, pp. 252-261
-
-
Tang, X.1
Kirkpatrick, B.2
Thomas, S.3
Song, G.4
Amato, N.M.5
-
47
-
-
0002856165
-
Some matroids from discrete applied geometry
-
W. Whiteley. Some matroids from discrete applied geometry. Contemp. Math., 197:171-311, 1996.
-
(1996)
Contemp. Math.
, vol.197
, pp. 171-311
-
-
Whiteley, W.1
-
48
-
-
33745790193
-
Incremental map generation
-
Parasol Lab, Dept. of Computer Science, Texas A&M University, Sep
-
D. Xie, S. Thomas, J.-M. Lien, and N. M. Amato. Incremental map generation. Technical Report TR05-006, Parasol Lab, Dept. of Computer Science, Texas A&M University, Sep 2005.
-
(2005)
Technical Report
, vol.TR05-006
-
-
Xie, D.1
Thomas, S.2
Lien, J.-M.3
Amato, N.M.4
-
49
-
-
2342471328
-
Simulation of and ensemble of conformational transitions in a united-residue model of calmodulin
-
D. M. Zuckerman. Simulation of and ensemble of conformational transitions in a united-residue model of calmodulin. J. Phys. Chem, 108:5127-5137, 2004.
-
(2004)
J. Phys. Chem
, vol.108
, pp. 5127-5137
-
-
Zuckerman, D.M.1
|