-
1
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
2
-
-
0035956886
-
Recent improvements in prediction of protein structure by global optimization of a potential energy function
-
Pillardy J, Czaplewski C, Liwo A, Lee J, Ripoll DR, Kamierkiewicz R, Oldziej S, Wedemeyer WJ, Gibson KD, Arnautova YA, Saunders J, Ye Y-J, Scheraga HA. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci USA 2001;98:2329-2333.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 2329-2333
-
-
Pillardy, J.1
Czaplewski, C.2
Liwo, A.3
Lee, J.4
Ripoll, D.R.5
Kamierkiewicz, R.6
Oldziej, S.7
Wedemeyer, W.J.8
Gibson, K.D.9
Arnautova, Y.A.10
Saunders, J.11
Ye, Y.-J.12
Scheraga, H.A.13
-
4
-
-
0642285282
-
Reproducible protein folding with the stochastic tunneling method
-
Schug A, Herges T, Wenzel W. Reproducible protein folding with the stochastic tunneling method. Phys Rev Lett 2003;91:158102.
-
(2003)
Phys Rev Lett
, vol.91
, pp. 158102
-
-
Schug, A.1
Herges, T.2
Wenzel, W.3
-
6
-
-
0344304436
-
Atomically detailed folding simulation of the b domain of staphylococcal protein a from random structures
-
Vila JA, Ripoll DR, Scheraga HA. Atomically detailed folding simulation of the b domain of staphylococcal protein a from random structures. Proc Natl Acad Sci USA 2004;100:14812-14816.
-
(2004)
Proc Natl Acad Sci USA
, vol.100
, pp. 14812-14816
-
-
Vila, J.A.1
Ripoll, D.R.2
Scheraga, H.A.3
-
7
-
-
0042311829
-
Global optimization by energy landscape paving
-
Hansmann UHE. Global optimization by energy landscape paving. Phys Rev Lett 2002;88:068105.
-
(2002)
Phys Rev Lett
, vol.88
, pp. 068105
-
-
Hansmann, U.H.E.1
-
8
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews J. Drug discovery: a historical perspective. Science 2000;287:1960-1964.
-
(2000)
Science
, vol.287
, pp. 1960-1964
-
-
Drews, J.1
-
9
-
-
0037424459
-
Application of the stochastic tunneling method to high throughput screening
-
Merlitz H, Burghardt B, Wenzel W. Application of the stochastic tunneling method to high throughput screening. Chem Phys Lett 2003;370:68-73.
-
(2003)
Chem Phys Lett
, vol.370
, pp. 68-73
-
-
Merlitz, H.1
Burghardt, B.2
Wenzel, W.3
-
11
-
-
0035703089
-
Rosetta in casp4: Progress in ab-initio protein structure prediction
-
Bonneau R, Tsui J, Ruczinski I, Chivian D, Strauss CME, Baker D. Rosetta in casp4: progress in ab-initio protein structure prediction. Proteins 2001;45:119-126.
-
(2001)
Proteins
, vol.45
, pp. 119-126
-
-
Bonneau, R.1
Tsui, J.2
Ruczinski, I.3
Chivian, D.4
Strauss, C.M.E.5
Baker, D.6
-
12
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
13
-
-
0037038372
-
Absolute comparison of simulated and experimental protein folding dynamics
-
Snow CD, Nguyen H, Panda VS, Gruebele M. Absolute comparison of simulated and experimental protein folding dynamics. Nature 2002;420:102-106.
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Panda, V.S.3
Gruebele, M.4
-
14
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C, Strockbine B, Roitberg A. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002;124:11258-11259.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.3
-
15
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
16
-
-
0023430366
-
Monte Carlo minimization approach to the multiple minima problem in protein folding
-
Li Z, Scheraga HA. Monte Carlo minimization approach to the multiple minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 6611-6615
-
-
Li, Z.1
Scheraga, H.A.2
-
17
-
-
0037133165
-
A method for optimising potential energy functions by a hierarchical design of the potential energy landscape
-
Liwo A, Arlukowicz P, Czaplewski C, Oldizeij S, Pillardy J, Scheraga HA. A method for optimising potential energy functions by a hierarchical design of the potential energy landscape. Proc Natl Acad Sci USA 2002;99:1937-1942.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1937-1942
-
-
Liwo, A.1
Arlukowicz, P.2
Czaplewski, C.3
Oldizeij, S.4
Pillardy, J.5
Scheraga, H.A.6
-
18
-
-
10344236244
-
Development of an all-atom forcefield for tertiary structure prediction of helical proteins
-
In press
-
Herges T, Wenzel W. Development of an all-atom forcefield for tertiary structure prediction of helical proteins. Biophysical Journal. In press.
-
Biophysical Journal
-
-
Herges, T.1
Wenzel, W.2
-
19
-
-
0034700249
-
Biochemical and structural analysis of the interaction between the uba(2) domain of the dna repair protein hhr23a and hiv-1 vpr
-
Withers-Ward ES, Mueller TD, Chen IS, Feigon J. Biochemical and structural analysis of the interaction between the uba(2) domain of the dna repair protein hhr23a and hiv-1 vpr. Biochemistry 2000;39:14103-14112.
-
(2000)
Biochemistry
, vol.39
, pp. 14103-14112
-
-
Withers-Ward, E.S.1
Mueller, T.D.2
Chen, I.S.3
Feigon, J.4
-
20
-
-
0036308140
-
Stochastic optimisation methods for biomolecular structure prediction
-
Herges T, Merlitz H, Wenzel W. Stochastic optimisation methods for biomolecular structure prediction. J Assoc Lab Autom 2002;7:98-104.
-
(2002)
J Assoc Lab Autom
, vol.7
, pp. 98-104
-
-
Herges, T.1
Merlitz, H.2
Wenzel, W.3
-
21
-
-
0027955787
-
Biased probability Monte Carlo conformation searches and electrostatic calculations for peptides and proteins
-
Abagyan R, Totrov M. Biased probability Monte Carlo conformation searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983-1002.
-
(1994)
J Mol Biol
, vol.235
, pp. 983-1002
-
-
Abagyan, R.1
Totrov, M.2
-
22
-
-
4544246504
-
Low energy conformations of a three helix peptide in an all-atom biomolecular forcefield
-
Herges T, Schug A, Burghardt B, Wenzel W. Low energy conformations of a three helix peptide in an all-atom biomolecular forcefield. Int J Quantum Chem 2004;99:854-863.
-
(2004)
Int J Quantum Chem
, vol.99
, pp. 854-863
-
-
Herges, T.1
Schug, A.2
Burghardt, B.3
Wenzel, W.4
-
23
-
-
0028960071
-
Role of electrostatic screening in determining protein main chain conformational preferences
-
Avbelj F, Moult J. Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry 1995;34:755-764.
-
(1995)
Biochemistry
, vol.34
, pp. 755-764
-
-
Avbelj, F.1
Moult, J.2
-
24
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
25
-
-
0026076664
-
Extracting hydrophobic free energies from experimental data:relationship to protein folding and theoretical models
-
Sharp KA, Nicholls A, Friedman R, Honig B. Extracting hydrophobic free energies from experimental data:relationship to protein folding and theoretical models. Biochemistry 1991;30:9686-9697.
-
(1991)
Biochemistry
, vol.30
, pp. 9686-9697
-
-
Sharp, K.A.1
Nicholls, A.2
Friedman, R.3
Honig, B.4
-
26
-
-
0242618215
-
Stochastic optimization methods for structure prediction of biomolecular nanoscale systems
-
Herges T, Schug A, Merlitz H, Wenzel W. Stochastic optimization methods for structure prediction of biomolecular nanoscale systems. Nanotechnology 2003;14:1161-1167.
-
(2003)
Nanotechnology
, vol.14
, pp. 1161-1167
-
-
Herges, T.1
Schug, A.2
Merlitz, H.3
Wenzel, W.4
-
29
-
-
0142013225
-
Numerical comparison of three recently proposed algorithms in the protein folding problem
-
Hansmann UHE, Okamoto Y. Numerical comparison of three recently proposed algorithms in the protein folding problem. J Comput Chem 1997;18:920-933.
-
(1997)
J Comput Chem
, vol.18
, pp. 920-933
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
31
-
-
0042171838
-
Parallel tempering simulations of HP-36
-
Lin CY, Hu CK, Hansmann UH. Parallel tempering simulations of HP-36. Proteins 2003;53:436-445.
-
(2003)
Proteins
, vol.53
, pp. 436-445
-
-
Lin, C.Y.1
Hu, C.K.2
Hansmann, U.H.3
-
32
-
-
0001616080
-
Ab initio replica-exchange Monte Carlo method for cluster studies
-
Sugita Y, Okamoto Y. Ab initio replica-exchange Monte Carlo method for cluster studies. Chem Phys Lett 1999;314:141-151.
-
(1999)
Chem Phys Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
33
-
-
0037456298
-
The complete folding pathway of a protein from nanoseconds to microseconds
-
Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SMV, Alonso DOV, Daggett V, Fersht AR. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 2003;421:863-867.
-
(2003)
Nature
, vol.421
, pp. 863-867
-
-
Mayor, U.1
Guydosh, N.R.2
Johnson, C.M.3
Grossmann, J.G.4
Sato, S.5
Jas, G.S.6
Freund, S.M.V.7
Alonso, D.O.V.8
Daggett, V.9
Fersht, A.R.10
-
34
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein a
-
Garcia AE, Onuchic N. Folding a protein in a computer: an atomic description of the folding/unfolding of protein a. Proc Natl Acad Sci USA 2003;100:13898-13903.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, N.2
-
35
-
-
1442287309
-
Comparisons of force fields for proteins by generalized-ensemble simulations
-
Yoda T, Sugita Y, Okamoto Y. Comparisons of force fields for proteins by generalized-ensemble simulations. Chem Phys Lett 2004;386:460-467.
-
(2004)
Chem Phys Lett
, vol.386
, pp. 460-467
-
-
Yoda, T.1
Sugita, Y.2
Okamoto, Y.3
-
36
-
-
21144456638
-
Protein structure prediction with stochastic optimization methods: Folding and misfolding the villin headpiece
-
Herges T, Schug A, Wenzel W. Protein structure prediction with stochastic optimization methods: folding and misfolding the villin headpiece. Lecture Notes in Computational Science. 2004;3045:454-464.
-
(2004)
Lecture Notes in Computational Science
, vol.3045
, pp. 454-464
-
-
Herges, T.1
Schug, A.2
Wenzel, W.3
-
37
-
-
1542297762
-
Solvation in protein folding analysis: Combination of theoretical and experimental approaches
-
Fernandez-Escamilla AM, Cheung MS, Vega MC, Wilmanns M, Onuchic JN, Serrano L. Solvation in protein folding analysis: combination of theoretical and experimental approaches. Proc Natl Acad Sci USA 2004;101:2834-2839.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 2834-2839
-
-
Fernandez-Escamilla, A.M.1
Cheung, M.S.2
Vega, M.C.3
Wilmanns, M.4
Onuchic, J.N.5
Serrano, L.6
|