-
1
-
-
0038148710
-
Conformational diversity and protein evolution - a 60-year-old hypothesis revisited
-
10.1016/S0968-0004(03)00135-X, 12878003
-
James LC, Tawfik DS. Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem Sci 2003, 28:361-368. 10.1016/S0968-0004(03)00135-X, 12878003.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 361-368
-
-
James, L.C.1
Tawfik, D.S.2
-
2
-
-
0033048066
-
Moonlighting proteins
-
10.1016/S0968-0004(98)01335-8, 10087914
-
Jeffery CJ. Moonlighting proteins. Trends Biochem Sci 1999, 24:8-11. 10.1016/S0968-0004(98)01335-8, 10087914.
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 8-11
-
-
Jeffery, C.J.1
-
3
-
-
0037396292
-
Enzymes with extra talents: moonlighting functions and catalytic promiscuity
-
10.1016/S1367-5931(03)00032-2, 12714060
-
Copley SD. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol 2003, 7:265-272. 10.1016/S1367-5931(03)00032-2, 12714060.
-
(2003)
Curr Opin Chem Biol
, vol.7
, pp. 265-272
-
-
Copley, S.D.1
-
4
-
-
0037470496
-
Antibody Multispecificity Mediated by Conformational Diversity
-
James LC, Roversi P, Tawfik DS. Antibody Multispecificity Mediated by Conformational Diversity. Science 2003, 229:1362-1367.
-
(2003)
Science
, vol.229
, pp. 1362-1367
-
-
James, L.C.1
Roversi, P.2
Tawfik, D.S.3
-
5
-
-
0035188466
-
Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution
-
10.1110/ps.ps.14601, 2374036, 11714928
-
James LC, Tawfik DS. Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution. Protein Sci 2001, 10:2600-2607. 10.1110/ps.ps.14601, 2374036, 11714928.
-
(2001)
Protein Sci
, vol.10
, pp. 2600-2607
-
-
James, L.C.1
Tawfik, D.S.2
-
6
-
-
1842298212
-
From Levinthal to pathways to funnels
-
10.1038/nsb0197-10, 8989315
-
Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struct Biol 1997, 4:10-19. 10.1038/nsb0197-10, 8989315.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
7
-
-
0029898244
-
Global properties of the mapping between local amino acid sequence and local structure in proteins
-
10.1073/pnas.93.12.5814, 39144, 8650175
-
Han KF, Baker D. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc Natl Acad Sci USA 1996, 93:5814-5818. 10.1073/pnas.93.12.5814, 39144, 8650175.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 5814-5818
-
-
Han, K.F.1
Baker, D.2
-
8
-
-
0001079105
-
On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations
-
10.1073/pnas.81.4.1075, 344767, 6422466
-
Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 1984, 81:1075-1078. 10.1073/pnas.81.4.1075, 344767, 6422466.
-
(1984)
Proc Natl Acad Sci USA
, vol.81
, pp. 1075-1078
-
-
Kabsch, W.1
Sander, C.2
-
9
-
-
0031871068
-
Chameleon sequences in the PDB
-
10.1093/protein/11.6.411, 9725618
-
Mezei M. Chameleon sequences in the PDB. Protein Eng 1998, 11:411-414. 10.1093/protein/11.6.411, 9725618.
-
(1998)
Protein Eng
, vol.11
, pp. 411-414
-
-
Mezei, M.1
-
10
-
-
0029865623
-
Context-dependent secondary structure formation of a designed protein sequence
-
10.1038/380730a0, 8614471
-
Minor DLJ, Kim PS. Context-dependent secondary structure formation of a designed protein sequence. Nature 1996, 380:730-734. 10.1038/380730a0, 8614471.
-
(1996)
Nature
, vol.380
, pp. 730-734
-
-
Minor, D.L.J.1
Kim, P.S.2
-
11
-
-
0033815822
-
Understanding the sequence determinants of conformational switching using protein design
-
10.1110/ps.9.9.1651, 2144699, 11045612
-
Dalal S, Regan L. Understanding the sequence determinants of conformational switching using protein design. Protein Sci 2000, 9:1651-1659. 10.1110/ps.9.9.1651, 2144699, 11045612.
-
(2000)
Protein Sci
, vol.9
, pp. 1651-1659
-
-
Dalal, S.1
Regan, L.2
-
12
-
-
0027253445
-
A spring-loaded mechanism for the conformational change of influenza hemagglutinin
-
10.1016/0092-8674(93)90260-W, 8500173
-
Carr CM, Kim PS. A spring-loaded mechanism for the conformational change of influenza hemagglutinin. Cell 1993, 73:823-832. 10.1016/0092-8674(93)90260-W, 8500173.
-
(1993)
Cell
, vol.73
, pp. 823-832
-
-
Carr, C.M.1
Kim, P.S.2
-
13
-
-
0030342681
-
Conformational switching in designed peptides: The helix/sheet transition
-
10.1016/S1359-0278(96)00018-1, 9079369
-
Cerpa R, Cohen FE, Kuntz ID. Conformational switching in designed peptides: The helix/sheet transition. Fold Des 1996, 1:91-101. 10.1016/S1359-0278(96)00018-1, 9079369.
-
(1996)
Fold Des
, vol.1
, pp. 91-101
-
-
Cerpa, R.1
Cohen, F.E.2
Kuntz, I.D.3
-
14
-
-
0030587932
-
An α to β conformational switch in EF-Tu
-
10.1016/S0969-2126(96)00123-2, 8939740
-
Abel K, Yoder MD, Hilgenfeld R, Jurnak F. An α to β conformational switch in EF-Tu. Structure 1996, 4:1153-1159. 10.1016/S0969-2126(96)00123-2, 8939740.
-
(1996)
Structure
, vol.4
, pp. 1153-1159
-
-
Abel, K.1
Yoder, M.D.2
Hilgenfeld, R.3
Jurnak, F.4
-
15
-
-
0031713107
-
Conversion of a β-strand to an α-helix induced by a single-site mutation observed in the crystal structure of Fis mutant Pro26Ala
-
10.1002/pro.5560070904, 2144158, 9761469
-
Yang WZ, Ko TP, Corselli L, Johnson RC, Yuan HS. Conversion of a β-strand to an α-helix induced by a single-site mutation observed in the crystal structure of Fis mutant Pro26Ala. Protein Sci 1998, 7:1875-1883. 10.1002/pro.5560070904, 2144158, 9761469.
-
(1998)
Protein Sci
, vol.7
, pp. 1875-1883
-
-
Yang, W.Z.1
Ko, T.P.2
Corselli, L.3
Johnson, R.C.4
Yuan, H.S.5
-
16
-
-
4444340508
-
The solution structure of a chimeric LEKTI domain reveals a chameleon sequence
-
10.1021/bi0492399, 15366933
-
Tidow H, Lauber T, Vitzithum K, Sommerhoff CP, Rosch P, Marx UC. The solution structure of a chimeric LEKTI domain reveals a chameleon sequence. Biochemistry 2004, 43:11238-11247. 10.1021/bi0492399, 15366933.
-
(2004)
Biochemistry
, vol.43
, pp. 11238-11247
-
-
Tidow, H.1
Lauber, T.2
Vitzithum, K.3
Sommerhoff, C.P.4
Rosch, P.5
Marx, U.C.6
-
17
-
-
0032006678
-
The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways
-
10.1016/S0959-440X(98)80016-X, 9519302
-
Kelly JW. The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. Curr Opin Struct Biol 1998, 8:101-106. 10.1016/S0959-440X(98)80016-X, 9519302.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 101-106
-
-
Kelly, J.W.1
-
18
-
-
0034718157
-
Alzheimer's amyloid fibrils: structure and assembly
-
Serpell LC. Alzheimer's amyloid fibrils: structure and assembly. Biochim Biophys Acta 2000, 1502:16-30.
-
(2000)
Biochim Biophys Acta
, vol.1502
, pp. 16-30
-
-
Serpell, L.C.1
-
19
-
-
0018110116
-
Prediction of the secondary structure of proteins from their amino acid sequence
-
Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 1978, 47:45-148.
-
(1978)
Adv Enzymol Relat Areas Mol Biol
, vol.47
, pp. 45-148
-
-
Chou, P.Y.1
Fasman, G.D.2
-
20
-
-
0028568650
-
Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales
-
10.1002/prot.340200403, 7731949
-
Munoz V, Serrano L. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins 1994, 20:301-311. 10.1002/prot.340200403, 7731949.
-
(1994)
Proteins
, vol.20
, pp. 301-311
-
-
Munoz, V.1
Serrano, L.2
-
21
-
-
0025260032
-
Side chain contributions to the stability of α-helical structure in peptides
-
10.1126/science.2237416, 2237416
-
Lyu PC, Liff MI, Marky LA, Kallenbach NR. Side chain contributions to the stability of α-helical structure in peptides. Science 1990, 250:669-673. 10.1126/science.2237416, 2237416.
-
(1990)
Science
, vol.250
, pp. 669-673
-
-
Lyu, P.C.1
Liff, M.I.2
Marky, L.A.3
Kallenbach, N.R.4
-
22
-
-
0025222978
-
A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
-
10.1126/science.2237415, 2237415
-
O'Neil KT, DeGrado WF. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 1990, 250:646-651. 10.1126/science.2237415, 2237415.
-
(1990)
Science
, vol.250
, pp. 646-651
-
-
O'Neil, K.T.1
DeGrado, W.F.2
-
23
-
-
0025253106
-
Relative helix-forming tendencies of nonpolar amino acids
-
10.1038/344268a0, 2314462
-
Padmanabhan S, Marqusee S, Ridgeway T, Laue TM, Baldwin RL. Relative helix-forming tendencies of nonpolar amino acids. Nature 1990, 344:268-270. 10.1038/344268a0, 2314462.
-
(1990)
Nature
, vol.344
, pp. 268-270
-
-
Padmanabhan, S.1
Marqusee, S.2
Ridgeway, T.3
Laue, T.M.4
Baldwin, R.L.5
-
24
-
-
0027411181
-
Thermodynamic β-sheet propensities measured using a zinc-finger host peptide
-
10.1038/362267a0, 8459852
-
Kim CA, Berg JM. Thermodynamic β-sheet propensities measured using a zinc-finger host peptide. Nature 1993, 362:267-270. 10.1038/362267a0, 8459852.
-
(1993)
Nature
, vol.362
, pp. 267-270
-
-
Kim, C.A.1
Berg, J.M.2
-
25
-
-
0027236794
-
Structural basis of amino acid α helix propensity
-
10.1126/science.8503008, 8503008
-
Blaber M, Zhang XJ, Matthews BW. Structural basis of amino acid α helix propensity. Science 1993, 260:1637-1640. 10.1126/science.8503008, 8503008.
-
(1993)
Science
, vol.260
, pp. 1637-1640
-
-
Blaber, M.1
Zhang, X.J.2
Matthews, B.W.3
-
26
-
-
0028176595
-
Measurement of the β-sheet-forming propensities of amino acids
-
10.1038/367660a0, 8107853
-
Minor DLJ, Kim PS. Measurement of the β-sheet-forming propensities of amino acids. Nature 1994, 367:660-663. 10.1038/367660a0, 8107853.
-
(1994)
Nature
, vol.367
, pp. 660-663
-
-
Minor, D.L.J.1
Kim, P.S.2
-
27
-
-
0028175780
-
A thermodynamic scale for the β-sheet forming tendencies of the amino acids
-
10.1021/bi00184a020, 8180173
-
Smith CK, Withka JM, Regan L. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 1994, 33:5510-5517. 10.1021/bi00184a020, 8180173.
-
(1994)
Biochemistry
, vol.33
, pp. 5510-5517
-
-
Smith, C.K.1
Withka, J.M.2
Regan, L.3
-
28
-
-
0028178865
-
α-helix-forming propensities in peptides and proteins
-
10.1002/prot.340190202, 8090712
-
Creamer TP, Rose GD. α-helix-forming propensities in peptides and proteins. Proteins 1994, 19:85-97. 10.1002/prot.340190202, 8090712.
-
(1994)
Proteins
, vol.19
, pp. 85-97
-
-
Creamer, T.P.1
Rose, G.D.2
-
29
-
-
0026608073
-
Environment affects amino acid preference for secondary structure
-
10.1073/pnas.89.10.4462, 49102, 1584778
-
Zhong L, Johnson WCJ. Environment affects amino acid preference for secondary structure. Proc Natl Acad Sci USA 1992, 89:4462-4465. 10.1073/pnas.89.10.4462, 49102, 1584778.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 4462-4465
-
-
Zhong, L.1
Johnson, W.C.J.2
-
30
-
-
0028279006
-
Importance of environment in determining secondary structure in proteins
-
10.1021/bi00174a019, 8117668
-
Waterhous DV, Johnson WCJ. Importance of environment in determining secondary structure in proteins. Biochemistry 1994, 33:2121-2128. 10.1021/bi00174a019, 8117668.
-
(1994)
Biochemistry
, vol.33
, pp. 2121-2128
-
-
Waterhous, D.V.1
Johnson, W.C.J.2
-
31
-
-
0028890190
-
Induced conformational states of amphipathic peptides in aqueous/lipid environments
-
10.1016/S0006-3495(95)80194-3, 1281694, 7711261
-
Blondelle SE, Ostresh JM, Houghten RA, Perez-Paya E. Induced conformational states of amphipathic peptides in aqueous/lipid environments. Biophys J 1995, 68:351-359. 10.1016/S0006-3495(95)80194-3, 1281694, 7711261.
-
(1995)
Biophys J
, vol.68
, pp. 351-359
-
-
Blondelle, S.E.1
Ostresh, J.M.2
Houghten, R.A.3
Perez-Paya, E.4
-
32
-
-
0035782925
-
Review: protein secondary structure prediction continues to rise
-
10.1006/jsbi.2001.4336, 11551180
-
Rost B. Review: protein secondary structure prediction continues to rise. J Struct Biol 2001, 134:204-218. 10.1006/jsbi.2001.4336, 11551180.
-
(2001)
J Struct Biol
, vol.134
, pp. 204-218
-
-
Rost, B.1
-
33
-
-
0027448801
-
Origins of structural diversity within sequentially identical hexapeptides
-
10.1002/pro.5560021213, 2142335, 8298461
-
Cohen BI, Presnell SR, Cohen FE. Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 1993, 2:2134-2145. 10.1002/pro.5560021213, 2142335, 8298461.
-
(1993)
Protein Sci
, vol.2
, pp. 2134-2145
-
-
Cohen, B.I.1
Presnell, S.R.2
Cohen, F.E.3
-
34
-
-
0034333229
-
An analysis of the helix-to-strand transition between peptides with identical sequenc
-
10.1002/1097-0134(20001101)41:2<248::AID-PROT90>3.0.CO;2-J, 10966577
-
Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. An analysis of the helix-to-strand transition between peptides with identical sequenc. Proteins 2000, 41:248-256. 10.1002/1097-0134(20001101)41:2<248::AID-PROT90>3.0.CO;2-J, 10966577.
-
(2000)
Proteins
, vol.41
, pp. 248-256
-
-
Zhou, X.1
Alber, F.2
Folkers, G.3
Gonnet, G.H.4
Chelvanayagam, G.5
-
35
-
-
0142241182
-
On the properties and sequence context of structurally ambivalent fragments in proteins
-
10.1110/ps.03209703, 2366964, 14573856
-
Kuznetsov IB, Rackovsky S. On the properties and sequence context of structurally ambivalent fragments in proteins. Protein Sci 2003, 12:2420-2433. 10.1110/ps.03209703, 2366964, 14573856.
-
(2003)
Protein Sci
, vol.12
, pp. 2420-2433
-
-
Kuznetsov, I.B.1
Rackovsky, S.2
-
36
-
-
34247223063
-
Analysis of Chameleon Sequences and Their Implications in Biological Processes
-
10.1002/prot.21285, 17299764
-
Guo J, Jaromczyk JW, Xu Y. Analysis of Chameleon Sequences and Their Implications in Biological Processes. Proteins 2007, 67:548-558. 10.1002/prot.21285, 17299764.
-
(2007)
Proteins
, vol.67
, pp. 548-558
-
-
Guo, J.1
Jaromczyk, J.W.2
Xu, Y.3
-
37
-
-
0028205447
-
Enlarged representative set of protein structures
-
10.1002/pro.5560030317, 2142698, 8019422
-
Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994, 3:522-524. 10.1002/pro.5560030317, 2142698, 8019422.
-
(1994)
Protein Sci
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
38
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
39
-
-
0015967881
-
Conformational Parameters for Amino Acids in Helical, β-Sheet, and Random Coil Regions Calculated from Proteins
-
10.1021/bi00699a001, 4358939
-
Chou PY, Fasman GD. Conformational Parameters for Amino Acids in Helical, β-Sheet, and Random Coil Regions Calculated from Proteins. Biochemistry 1974, 13:211-222. 10.1021/bi00699a001, 4358939.
-
(1974)
Biochemistry
, vol.13
, pp. 211-222
-
-
Chou, P.Y.1
Fasman, G.D.2
-
40
-
-
0023193211
-
Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures: Strategies for protein folding and a guide for site-directed mutagenesis
-
10.1016/0022-2836(87)90127-6, 3681998
-
Argos P. Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures: Strategies for protein folding and a guide for site-directed mutagenesis. J Mol Biol 1987, 197:331-348. 10.1016/0022-2836(87)90127-6, 3681998.
-
(1987)
J Mol Biol
, vol.197
, pp. 331-348
-
-
Argos, P.1
-
41
-
-
0020997912
-
Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features
-
10.1002/bip.360221211, 6667333
-
Kabsch W, Sander C. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 1983, 22:2577-2637. 10.1002/bip.360221211, 6667333.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
42
-
-
0000076259
-
DETERMINATION OF THE PARAMETERS FOR HELIX FORMATION IN POLY-y-BENZYL-L-GLUTAMATE
-
10.1073/pnas.45.11.1601, 222768, 16590552
-
Zim BH, Doty P, Iso K. DETERMINATION OF THE PARAMETERS FOR HELIX FORMATION IN POLY-y-BENZYL-L-GLUTAMATE. Proc Natl Acad Sci USA 1959, 45:1601-1607. 10.1073/pnas.45.11.1601, 222768, 16590552.
-
(1959)
Proc Natl Acad Sci USA
, vol.45
, pp. 1601-1607
-
-
Zim, B.H.1
Doty, P.2
Iso, K.3
-
44
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
10.1016/S0022-2836(77)80200-3, 875032
-
Bernstein FC, Koetzle TF, Williams GJB, Meyer EFJ, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The protein data bank: A computer-based archival file for macromolecular structures. J Mol Biol 1977, 112:535-542. 10.1016/S0022-2836(77)80200-3, 875032.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.J.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
45
-
-
0043180474
-
PISCES: a protein sequence culling server
-
10.1093/bioinformatics/btg224, 12912846
-
Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003, 19:1589-1591. 10.1093/bioinformatics/btg224, 12912846.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
46
-
-
1542346418
-
A novel method for protein secondary structure prediction using dual-layer SVM and profiles
-
10.1002/prot.10634, 14997569
-
Guo J, Chen H, Sun ZR, Lin YL. A novel method for protein secondary structure prediction using dual-layer SVM and profiles. Proteins 2004, 54:738-743. 10.1002/prot.10634, 14997569.
-
(2004)
Proteins
, vol.54
, pp. 738-743
-
-
Guo, J.1
Chen, H.2
Sun, Z.R.3
Lin, Y.L.4
-
47
-
-
0035957531
-
A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
-
10.1006/jmbi.2001.4580, 11327775
-
Hua SJ, Sun ZR. A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach. J Mol Biol 2001, 308:397-407. 10.1006/jmbi.2001.4580, 11327775.
-
(2001)
J Mol Biol
, vol.308
, pp. 397-407
-
-
Hua, S.J.1
Sun, Z.R.2
-
48
-
-
0141593924
-
Protein secondary structure prediction based on an improved support vector machines approach
-
10.1093/protein/gzg072, 12968073
-
Kim H, Park H. Protein secondary structure prediction based on an improved support vector machines approach. Protein Eng 2003, 16:553-560. 10.1093/protein/gzg072, 12968073.
-
(2003)
Protein Eng
, vol.16
, pp. 553-560
-
-
Kim, H.1
Park, H.2
-
49
-
-
34247186195
-
-
University of California, San Francisco
-
Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA. AMBER 9 2006, University of California, San Francisco.
-
(2006)
AMBER 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
Walker, R.C.11
Zhang, W.12
Wang, B.13
Hayik, S.14
Roitberg, A.15
Seabra, G.16
Wong, K.F.17
Paesani, F.18
Wu, X.19
Brozell, S.20
Tsui, V.21
Gohlke, H.22
Yang, L.23
Tan, C.24
Mongan, J.25
Hornak, V.26
Cui, G.27
Beroza, P.28
Mathews, D.H.29
Schafmeister, C.30
Ross, W.S.31
Kollman, P.A.32
more..
-
50
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
10.1002/prot.21123, 16981200
-
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006, 65:712-725. 10.1002/prot.21123, 16981200.
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
51
-
-
67649494492
-
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides
-
10.1021/jp901540t, 19514729
-
Best RB, Hummer G. Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides. J Phys Chem B 2009, 113:9004-9015. 10.1021/jp901540t, 19514729.
-
(2009)
J Phys Chem B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
52
-
-
33846823909
-
Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J Chem Phys 1993, 98:10089-11009.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-11009
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
53
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 1977, 23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
54
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984, 81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
DiNola, A.3
Haak, J.R.4
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