-
1
-
-
2342525085
-
Heterogeneity and inaccuracy in protein structures solved by x-ray crystallography
-
May
-
DePristo MA, de Bakker PI, Blundell TL. Heterogeneity and inaccuracy in protein structures solved by x-ray crystallography. Structure. 2004 May;12(5):831–8.
-
(2004)
Structure
, vol.12
, Issue.5
, pp. 831-838
-
-
Depristo, M.A.1
De Bakker, P.I.2
Blundell, T.L.3
-
2
-
-
0001099937
-
Traitement statistique des erreurs dans la determination des structures cristallines
-
Nov
-
Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallogr. 1952 Nov;5(6):802–10.
-
(1952)
Acta Crystallogr
, vol.5
, Issue.6
, pp. 802-810
-
-
Luzzati, V.1
-
4
-
-
0031853060
-
Protein dynamics from NMR
-
Jul
-
Kay LE. Protein dynamics from NMR. Nat Struct Biol. 1998 Jul;5 Suppl:513–7.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 513-517
-
-
Kay, L.E.1
-
5
-
-
0001645813
-
Phase improvement by multi-start simulated annealing refnement and structure-factor averaging
-
Oct
-
Rice LM, Shamoo Y, Brünger AT. Phase improvement by multi-start simulated annealing refnement and structure-factor averaging. J Appl Crystallogr. 1998 Oct;31(5):798–805.
-
(1998)
J Appl Crystallogr
, vol.31
, Issue.5
, pp. 798-805
-
-
Rice, L.M.1
Shamoo, Y.2
Brünger, A.T.3
-
6
-
-
85005537029
-
Thermal motion and conforma-tional disorder in protein crystal-structures: Comparison of multi-conformer and time-averaging models
-
Burling FT, Brünger AT. Thermal motion and conforma-tional disorder in protein crystal-structures: comparison of multi-conformer and time-averaging models. Isr J Chem. 1994;34:165–75.
-
(1994)
Isr J Chem
, vol.34
, pp. 165-175
-
-
Burling, F.T.1
Brünger, A.T.2
-
7
-
-
34548643898
-
Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm
-
Oct
-
Liu X, Jiang W, Jakana J, Chiu W. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J Struct Biol. 2007 Oct;160(1):11–27.
-
(2007)
J Struct Biol
, vol.160
, Issue.1
, pp. 11-27
-
-
Liu, X.1
Jiang, W.2
Jakana, J.3
Chiu, W.4
-
8
-
-
34548387498
-
Ensemble refnement of protein crystal structures: Validation and application
-
Sep
-
Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refnement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040–52.
-
(2007)
Structure
, vol.15
, Issue.9
, pp. 1040-1052
-
-
Levin, E.J.1
Kondrashov, D.A.2
Wesenberg, G.E.3
Phillips, G.N.4
-
9
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Jan 13
-
Lindorff-Larsen K, Best RB, DePristo MA, Dobson CM, Vendruscolo M. Simultaneous determination of protein structure and dynamics. Nature. 2005 Jan 13;433(7022):128–32.
-
(2005)
Nature
, vol.433
, Issue.7022
, pp. 128-132
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Depristo, M.A.3
Dobson, C.M.4
Vendruscolo, M.5
-
10
-
-
18744371588
-
Molecular dynamics and protein function
-
May 10
-
Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci U S A. 2005 May 10;102(19):6679–85.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.19
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
11
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Apr
-
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol. 2009 Apr;19(2):120–7.
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.2
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
12
-
-
0029633167
-
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt M, Hirshberg M, Sharon R, Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput Phys Commun. 1995;91:215–31.
-
(1995)
Comput Phys Commun
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
13
-
-
67049155677
-
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
-
May
-
Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 2009 May;5(5):e1000393.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.5
-
-
Friedland, G.D.1
Lakomek, N.A.2
Griesinger, C.3
Meiler, J.4
Kortemme, T.5
-
14
-
-
33846818860
-
Protein structural variation in computational models and crystallographic data
-
Feb
-
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips GN Jr. Protein structural variation in computational models and crystallographic data. Structure. 2007 Feb;15(2):169–77.
-
(2007)
Structure
, vol.15
, Issue.2
, pp. 169-177
-
-
Kondrashov, D.A.1
Van Wynsberghe, A.W.2
Bannen, R.M.3
Cui, Q.4
Phillips, G.N.5
-
15
-
-
84863243858
-
Computational prediction of protein hot spot residues
-
Morrow JK, Zhang S. Computational prediction of protein hot spot residues. Curr Pharm Des. 2012;18(9):1255–65.
-
(2012)
Curr Pharm Des
, vol.18
, Issue.9
, pp. 1255-1265
-
-
Morrow, J.K.1
Zhang, S.2
-
16
-
-
79958064379
-
Challenges for the prediction of macromolecular interactions
-
Jun
-
Wass MN, David A, Sternberg MJ. Challenges for the prediction of macromolecular interactions. Curr Opin Struct Biol. 2011 Jun;21(3):382–90.
-
(2011)
Curr Opin Struct Biol
, vol.21
, Issue.3
, pp. 382-390
-
-
Wass, M.N.1
David, A.2
Sternberg, M.J.3
-
17
-
-
41949111630
-
Recent progress and future directions in protein-protein docking
-
Feb
-
Ritchie DW. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci. 2008 Feb;9(1):1–15.
-
(2008)
Curr Protein Pept Sci
, vol.9
, Issue.1
, pp. 1-15
-
-
Ritchie, D.W.1
-
18
-
-
74849104439
-
Dynamic proteomics in modeling of the living cell. Protein-protein interactions
-
Dec
-
Terentiev AA, Moldogazieva NT, Shaitan KV. Dynamic proteomics in modeling of the living cell. Protein-protein interactions. Biochemistry (Mosc). 2009 Dec;74(13):1586–607.
-
(2009)
Biochemistry (Mosc)
, vol.74
, Issue.13
, pp. 1586-1607
-
-
Terentiev, A.A.1
Moldogazieva, N.T.2
Shaitan, K.V.3
-
19
-
-
0036280661
-
Ligand binding affnities from MD simulations
-
Jun
-
Aqvist J, Luzhkov VB, Brandsdal BO. Ligand binding affnities from MD simulations. ACC Chem Res. 2002 Jun;35(6):358–65.
-
(2002)
ACC Chem Res
, vol.35
, Issue.6
, pp. 358-365
-
-
Aqvist, J.1
Luzhkov, V.B.2
Brandsdal, B.O.3
-
20
-
-
25844478436
-
In-silico screening using fexible ligand binding pockets: A molecular dynamics-based approach
-
Apr
-
Sivanesan D, Rajnarayanan RV, Doherty J, Pattabiraman N. In-silico screening using fexible ligand binding pockets: a molecular dynamics-based approach. J Comput Aided Mol Des. 2005 Apr;19(4):213–28.
-
(2005)
J Comput Aided Mol Des
, vol.19
, Issue.4
, pp. 213-228
-
-
Sivanesan, D.1
Rajnarayanan, R.V.2
Doherty, J.3
Pattabiraman, N.4
-
21
-
-
3342918929
-
Methods for molecular dynamics simulations of protein folding/unfolding in solution
-
Sep
-
Beck DA, Daggett V. Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods. 2004 Sep;34(1):112–20.
-
(2004)
Methods
, vol.34
, Issue.1
, pp. 112-120
-
-
Beck, D.A.1
Daggett, V.2
-
22
-
-
0242610902
-
All-atom simulations of protein folding and unfolding
-
Day R, Daggett V. All-atom simulations of protein folding and unfolding. Adv Protein Chem. 2003;66:373–403.
-
(2003)
Adv Protein Chem
, vol.66
, pp. 373-403
-
-
Day, R.1
Daggett, V.2
-
23
-
-
26444608613
-
Ensemble versus single-molecule protein unfolding
-
Sep 20
-
Day R, Daggett V. Ensemble versus single-molecule protein unfolding. Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13445–50.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.38
, pp. 13445-13450
-
-
Day, R.1
Daggett, V.2
-
24
-
-
84857733776
-
Computational drug design targeting protein-protein interactions
-
Bienstock RJ. Computational drug design targeting protein-protein interactions. Curr Pharm Des. 2012;18(9):1240–54.
-
(2012)
Curr Pharm Des
, vol.18
, Issue.9
, pp. 1240-1254
-
-
Bienstock, R.J.1
-
25
-
-
78049444154
-
Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles
-
Aug 26, pii
-
Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol. 2010 Aug 26;6(8): pii, e1000911.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.8
-
-
Kohn, J.E.1
Afonine, P.V.2
Ruscio, J.Z.3
Adams, P.D.4
-
26
-
-
84885162175
-
Ensemble-based interpretations of NMR structural data to describe protein internal dynamics
-
Aug 30
-
Ángyán AF, Gáspári Z. Ensemble-based interpretations of NMR structural data to describe protein internal dynamics. Molecules. 2013 Aug 30;18(9):10548–67.
-
(2013)
Molecules
, vol.18
, Issue.9
, pp. 10548-10567
-
-
Ángyán, A.F.1
Gáspári, Z.2
-
27
-
-
84896949718
-
NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions
-
Ghitti M, Musco G, Spitaleri A. NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions. Adv Exp Med Biol. 2014;805:271–304.
-
(2014)
Adv Exp Med Biol
, vol.805
, pp. 271-304
-
-
Ghitti, M.1
Musco, G.2
Spitaleri, A.3
-
28
-
-
84884284595
-
Fast real-time NMR methods for characterizing short-lived molecular states
-
Sep 16
-
Rennella E, Brutscher B. Fast real-time NMR methods for characterizing short-lived molecular states. Chemp-hyschem. 2013 Sep 16;14(13):3059–70.
-
(2013)
Chemp-hyschem
, vol.14
, Issue.13
, pp. 3059-3070
-
-
Rennella, E.1
Brutscher, B.2
-
29
-
-
84859622200
-
Effects of point substitutions on the structure of toxic Alzheimer’s β-amyloid channels: Atomic force microscopy and molecular dynamics simulations
-
Apr 10
-
Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R. Effects of point substitutions on the structure of toxic Alzheimer’s β-amyloid channels: atomic force microscopy and molecular dynamics simulations. Biochemistry. 2012 Apr 10;51(14):3031–8.
-
(2012)
Biochemistry
, vol.51
, Issue.14
, pp. 3031-3038
-
-
Connelly, L.1
Jang, H.2
Arce, F.T.3
Ramachandran, S.4
Kagan, B.L.5
Nussinov, R.6
Lal, R.7
-
30
-
-
84862896208
-
Cryo-electron microscopy modeling by the molecular dynamics fexible ftting method
-
Sep
-
Chan KY, Trabuco LG, Schreiner E, Schulten K. Cryo-electron microscopy modeling by the molecular dynamics fexible ftting method. Biopolymers. 2012 Sep;97(9):678–86.
-
(2012)
Biopolymers
, vol.97
, Issue.9
, pp. 678-686
-
-
Chan, K.Y.1
Trabuco, L.G.2
Schreiner, E.3
Schulten, K.4
-
31
-
-
84870565940
-
High data output method for 3-d correlative light-electron microscopy using ultrathin cryosections
-
Cortese K, Vicidomini G, Gagliani MC, Boccacci P, Di-aspro A, Tacchetti C. High data output method for 3-d correlative light-electron microscopy using ultrathin cryosections. Methods Mol Biol. 2013;950:417–37.
-
(2013)
Methods Mol Biol
, vol.950
, pp. 417-437
-
-
Cortese, K.1
Vicidomini, G.2
Gagliani, M.C.3
Boccacci, P.4
Di-Aspro, A.5
Tacchetti, C.6
-
32
-
-
84877004526
-
Enabling direct nanoscale observations of biological reactions with dynamic TEM
-
Feb
-
Evans JE, Browning ND. Enabling direct nanoscale observations of biological reactions with dynamic TEM. Microscopy (Oxf). 2013 Feb;62(1):147–56.
-
(2013)
Microscopy (Oxf)
, vol.62
, Issue.1
, pp. 147-156
-
-
Evans, J.E.1
Browning, N.D.2
-
33
-
-
84861231387
-
Study of mi-croheterogeneous environment of protein Human Serum Albumin by an extrinsic fuorescent reporter: A spectro-scopic study in combination with Molecular Docking and Molecular Dynamics Simulation
-
Jul 2
-
Jana S, Dalapati S, Ghosh S, Guchhait N. Study of mi-croheterogeneous environment of protein Human Serum Albumin by an extrinsic fuorescent reporter: a spectro-scopic study in combination with Molecular Docking and Molecular Dynamics Simulation. J Photochem Pho-tobiol B. 2012 Jul 2;112:48–58.
-
(2012)
J Photochem Pho-tobiol B
, vol.112
, pp. 48-58
-
-
Jana, S.1
Dalapati, S.2
Ghosh, S.3
Guchhait, N.4
-
34
-
-
84859924251
-
Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation
-
Apr 18
-
Lv C, Tan C, Qin M, Zou D, Cao Y, Wang W. Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation. Biophys J. 2012 Apr 18;102(8):1944–51.
-
(2012)
Biophys J
, vol.102
, Issue.8
, pp. 1944-1951
-
-
Lv, C.1
Tan, C.2
Qin, M.3
Zou, D.4
Cao, Y.5
Wang, W.6
-
35
-
-
65249122552
-
A unifed model of protein dynamics
-
Mar 31
-
Frauenfelder H, Chen G, Berendzen J, Fenimore PW, Jansson H, McMahon BH, Stroe IR, Swenson J, Young RD. A unifed model of protein dynamics. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5129–34.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.13
, pp. 5129-5134
-
-
Frauenfelder, H.1
Chen, G.2
Berendzen, J.3
Fenimore, P.W.4
Jansson, H.5
McMahon, B.H.6
Stroe, I.R.7
Swenson, J.8
Young, R.D.9
-
36
-
-
84864212825
-
Discovering free energy basins for macromolecular systems via guided multiscale simulation
-
Jul 26
-
Sereda YV, Singharoy AB, Jarrold MF, Ortoleva PJ. Discovering free energy basins for macromolecular systems via guided multiscale simulation. J Phys Chem B. 2012 Jul 26;116(29):8534–44.
-
(2012)
J Phys Chem B
, vol.116
, Issue.29
, pp. 8534-8544
-
-
Sereda, Y.V.1
Singharoy, A.B.2
Jarrold, M.F.3
Ortoleva, P.J.4
-
37
-
-
84908221627
-
Modelling dynamics in protein crystal structures by ensemble re-fnement
-
Dec 18
-
Burnley BT, Afonine PV, Adams PD, Gros P. Modelling dynamics in protein crystal structures by ensemble re-fnement. Elife. 2012 Dec 18;1:e00311.
-
(2012)
Elife
, vol.1
-
-
Burnley, B.T.1
Afonine, P.V.2
Adams, P.D.3
Gros, P.4
-
38
-
-
44649116524
-
Dy-nameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
-
Jun
-
Beck DA, Jonsson AL, Schaeffer RD, Scott KA, Day R, Toofanny RD, Alonso DO, Daggett V. Dy-nameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Eng Des Sel. 2008 Jun;21(6):353–68.
-
(2008)
Protein Eng Des Sel
, vol.21
, Issue.6
, pp. 353-368
-
-
Beck, D.A.1
Jonsson, A.L.2
Schaeffer, R.D.3
Scott, K.A.4
Day, R.5
Toofanny, R.D.6
Alonso, D.O.7
Daggett, V.8
-
39
-
-
56749176808
-
Dynameomics: Large-scale assessment of native protein fexibility
-
Dec
-
Benson NC, Daggett V. Dynameomics: large-scale assessment of native protein fexibility. Protein Sci. 2008 Dec;17(12):2038–50.
-
(2008)
Protein Sci
, vol.17
, Issue.12
, pp. 2038-2050
-
-
Benson, N.C.1
Daggett, V.2
-
40
-
-
44649152369
-
Dy-nameomics: A multi-dimensional analysis-optimized database for dynamic protein data
-
Jun
-
Kehl C, Simms AM, Toofanny RD, Daggett V. Dy-nameomics: a multi-dimensional analysis-optimized database for dynamic protein data. Protein Eng Des Sel. 2008 Jun;21(6):379–86.
-
(2008)
Protein Eng Des Sel
, vol.21
, Issue.6
, pp. 379-386
-
-
Kehl, C.1
Simms, A.M.2
Toofanny, R.D.3
Daggett, V.4
-
41
-
-
44649195146
-
Dynameomics: Design of a computational lab work-fow and scientifc data repository for protein simulations
-
Jun
-
Simms AM, Toofanny RD, Kehl C, Benson NC, Daggett V. Dynameomics: design of a computational lab work-fow and scientifc data repository for protein simulations. Protein Eng Des Sel. 2008 Jun;21(6):369–77.
-
(2008)
Protein Eng Des Sel
, vol.21
, Issue.6
, pp. 369-377
-
-
Simms, A.M.1
Toofanny, R.D.2
Kehl, C.3
Benson, N.C.4
Daggett, V.5
-
42
-
-
0036215711
-
Protein nucleation and crystallization by homologous protein thin flm template
-
Pechkova E, Nicolini C. Protein nucleation and crystallization by homologous protein thin flm template. J Cell Biochem. 2002;85(2):243–51.
-
(2002)
J Cell Biochem
, vol.85
, Issue.2
, pp. 243-251
-
-
Pechkova, E.1
Nicolini, C.2
-
43
-
-
1242338109
-
Protein nanocrystallography: A new approach to structural proteomics
-
Mar
-
Pechkova E, Nicolini C. Protein nanocrystallography: a new approach to structural proteomics. Trends Biotech-nol. 2004 Mar;22(3):117–22.
-
(2004)
Trends Biotech-nol
, vol.22
, Issue.3
, pp. 117-122
-
-
Pechkova, E.1
Nicolini, C.2
-
44
-
-
84885873003
-
Recombinant laccase: I. Enzyme cloning and characterization
-
Mar
-
Nicolini C, Bruzzese D, Cambria MT, Bragazzi NL, Pech-kova E. Recombinant laccase: I. Enzyme cloning and characterization. J Cell Biochem. 2013 Mar;114(3):599–605.
-
(2013)
J Cell Biochem
, vol.114
, Issue.3
, pp. 599-605
-
-
Nicolini, C.1
Bruzzese, D.2
Cambria, M.T.3
Bragazzi, N.L.4
Pech-Kova, E.5
-
45
-
-
84868120805
-
Recombinant laccase
-
Bragazzi NL, Pechkova E, Scudieri D, Terencio TB, Adami M, Nicolini C. Recombinant laccase: II. Medical biosensor. Crit Rev Eukaryot Gene Expr. 2012;22(3):197–203.
-
(2012)
II. Medical biosensor. Crit Rev Eukaryot Gene Expr.
, vol.22
, Issue.3
, pp. 197-203
-
-
Bragazzi, N.L.1
Pechkova, E.2
Scudieri, D.3
Terencio, T.B.4
Adami, M.5
Nicolini, C.6
-
46
-
-
84871681342
-
Prototypes of newly conceived inorganic and biological sensors for health and environmental applications
-
Dec 12
-
Nicolini C, Adami M, Sartore M, Bragazzi NL, Bavas-trello V, Spera R, Pechkova E. Prototypes of newly conceived inorganic and biological sensors for health and environmental applications. Sensors (Basel). 2012 Dec 12;12(12):17112–27.
-
(2012)
Sensors (Basel)
, vol.12
, Issue.12
, pp. 17112-17127
-
-
Nicolini, C.1
Adami, M.2
Sartore, M.3
Bragazzi, N.L.4
Bavas-Trello, V.5
Spera, R.6
Pechkova, E.7
-
47
-
-
84888066532
-
From nanobio-technology to organic and biological monitoring of health and environment for biosafety
-
Nicolini C, Bragazzi N, Pechkova E. From nanobio-technology to organic and biological monitoring of health and environment for biosafety. J Bioanal Biomed. 2013;5:108–17.
-
(2013)
J Bioanal Biomed
, vol.5
, pp. 108-117
-
-
Nicolini, C.1
Bragazzi, N.2
Pechkova, E.3
-
48
-
-
84867659106
-
Nanoproteomics enabling personalized nanomedicine
-
Oct
-
Nicolini C, Bragazzi N, Pechkova E. Nanoproteomics enabling personalized nanomedicine. Adv Drug Deliv Rev. 2012 Oct;64(13):1522–31.
-
(2012)
Adv Drug Deliv Rev
, vol.64
, Issue.13
, pp. 1522-1531
-
-
Nicolini, C.1
Bragazzi, N.2
Pechkova, E.3
-
51
-
-
77954905568
-
Domain organization and properties of LB lysozyme crystals down to submicron size
-
Jul
-
Pechkova E, Nicolini C. Domain organization and properties of LB lysozyme crystals down to submicron size. Anticancer Res. 2010 Jul;30(7):2745–8.
-
(2010)
Anticancer Res
, vol.30
, Issue.7
, pp. 2745-2748
-
-
Pechkova, E.1
Nicolini, C.2
-
52
-
-
70350217322
-
Radiation stability of proteinase K crystals grown by LB nanotemplate method
-
Dec
-
Pechkova E, Tripathi S, Ravelli RB, McSweeney S, Nicolini C. Radiation stability of proteinase K crystals grown by LB nanotemplate method. J Struct Biol. 2009 Dec;168(3):409–18.
-
(2009)
J Struct Biol
, vol.168
, Issue.3
, pp. 409-418
-
-
Pechkova, E.1
Tripathi, S.2
Ravelli, R.B.3
McSweeney, S.4
Nicolini, C.5
-
53
-
-
84903621858
-
A review of the strategies for obtaining high quality crystals utilizing nanotechnologies and space
-
Pechkova E, Bragazzi NL, Bozdaganyan M, Belmonte L, Nicolini C. A review of the strategies for obtaining high quality crystals utilizing nanotechnologies and space. Crit Rev Eukaryot Gene Expr. 2014;24(4):309–22.
-
(2014)
Crit Rev Eukaryot Gene Expr
, vol.24
, Issue.4
, pp. 309-322
-
-
Pechkova, E.1
Bragazzi, N.L.2
Bozdaganyan, M.3
Belmonte, L.4
Nicolini, C.5
-
54
-
-
80051903352
-
Lysozyme: A model protein for amyloid research
-
Swaminathan R, Ravi VK, Kumar S, Kumar MV, Chandra N. Lysozyme: a model protein for amyloid research. Adv Protein Chem Struct Biol. 2011;84:63–111.
-
(2011)
Adv Protein Chem Struct Biol
, vol.84
, pp. 63-111
-
-
Swaminathan, R.1
Ravi, V.K.2
Kumar, S.3
Kumar, M.V.4
Chandra, N.5
-
55
-
-
69949139818
-
Molecular dynamics simulations of hen egg white lysozyme adsorption at a charged solid surface
-
Sep 10
-
Kubiak K, Mulheran PA. Molecular dynamics simulations of hen egg white lysozyme adsorption at a charged solid surface. J Phys Chem B. 2009 Sep 10;113(36):12189–200.
-
(2009)
J Phys Chem B
, vol.113
, Issue.36
, pp. 12189-12200
-
-
Kubiak, K.1
Mulheran, P.A.2
-
56
-
-
33845329531
-
Structural analysis of human lysozyme using molecular dynamics simulations
-
Dec
-
Liu HL, Wu YC, Zhao JH, Fang HW, Ho Y. Structural analysis of human lysozyme using molecular dynamics simulations. J Biomol Struct Dyn. 2006 Dec;24(3):229–38.
-
(2006)
J Biomol Struct Dyn
, vol.24
, Issue.3
, pp. 229-238
-
-
Liu, H.L.1
Wu, Y.C.2
Zhao, J.H.3
Fang, H.W.4
Ho, Y.5
-
57
-
-
71349084072
-
Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K
-
Jan
-
Liu SQ, Meng ZH, Fu YX, Zhang KQ. Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K. J Mol Model. 2010 Jan;16(1):17–28.
-
(2010)
J Mol Model
, vol.16
, Issue.1
, pp. 17-28
-
-
Liu, S.Q.1
Meng, Z.H.2
Fu, Y.X.3
Zhang, K.Q.4
-
58
-
-
77957302449
-
Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K
-
Oct
-
Tao Y, Rao ZH, Liu SQ. Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. J Biomol Struct Dyn. 2010 Oct;28(2):143–58.
-
(2010)
J Biomol Struct Dyn
, vol.28
, Issue.2
, pp. 143-158
-
-
Tao, Y.1
Rao, Z.H.2
Liu, S.Q.3
-
59
-
-
84873445237
-
Kiwifruit proteins and enzymes: Actini-din and other significant proteins
-
Boland M. Kiwifruit proteins and enzymes: actini-din and other significant proteins. Adv Food Nutr Res. 2013;68:59–80.
-
(2013)
Adv Food Nutr Res
, vol.68
, pp. 59-80
-
-
Boland, M.1
-
60
-
-
84861333269
-
Controlling the aggregation and rate of release in order to improve insulin formulation: Molecular dynamics study of full-length insulin amyloid oligomer models
-
Mar
-
Berhanu WM, Masunov AE. Controlling the aggregation and rate of release in order to improve insulin formulation: molecular dynamics study of full-length insulin amyloid oligomer models. J Mol Model. 2012 Mar;18(3):1129–42.
-
(2012)
J Mol Model
, vol.18
, Issue.3
, pp. 1129-1142
-
-
Berhanu, W.M.1
Masunov, A.E.2
-
61
-
-
33645941402
-
The OPLS force feld for proteins. energy minimizations for crystals of cyclic peptides and Crambin
-
Jorgensen WL, Tirado-Rives J. The OPLS force feld for proteins. energy minimizations for crystals of cyclic peptides and Crambin. J Am Chem Soc. 1988;110(6):1657–66.
-
(1988)
J Am Chem Soc
, vol.110
, Issue.6
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
62
-
-
0029912748
-
Development and testing of the OPLS all-atom force feld on con-formational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force feld on con-formational energetics and properties of organic liquids. J Am Chem Soc. 1996;118(45):11225–36.
-
(1996)
J Am Chem Soc
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
63
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force feld for proteins via comparison to accurate quantum chemical calculations on peptides
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force feld for proteins via comparison to accurate quantum chemical calculations on peptides. J Phys Chem B. 2001;105(28):6474–87.
-
(2001)
J Phys Chem B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
64
-
-
0037041682
-
Effcient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations
-
Qian X, Schlick T. Effcient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations. J Chem Phys. 2002;116, 5971–83.
-
(2002)
J Chem Phys
, vol.116
, pp. 5971-5983
-
-
Qian, X.1
Schlick, T.2
-
65
-
-
0038997883
-
Optimal spline cutoffs for Coulomb and van der Waals interactions
-
Ding HQ, Karasawa N, Goddard III WA. Optimal spline cutoffs for Coulomb and van der Waals interactions. Chem Phys Lett. 1992 May;193(1–3):197–201.
-
(1992)
Chem Phys Lett
, vol.193
, Issue.1-3
, pp. 197-201
-
-
Ding, H.Q.1
Karasawa, N.2
Goddard, W.A.3
-
66
-
-
27344455355
-
Molecular dynamics in the isother-mal-isobaric ensemble: The requirement of a “shell” molecule. I. theory and phase-space analysis
-
Oct 22
-
Uline MJ, Corti DS. Molecular dynamics in the isother-mal-isobaric ensemble: the requirement of a “shell” molecule. I. theory and phase-space analysis. J Chem Phys. 2005 Oct 22;123(16):164101.
-
(2005)
J Chem Phys
, vol.123
, Issue.16
, pp. 164101
-
-
Uline, M.J.1
Corti, D.S.2
-
67
-
-
58449084188
-
Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity
-
Hong L, Lei J. Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity. J Polym Sci B Polym Phys. 2009;47:207–14.
-
(2009)
J Polym Sci B Polym Phys
, vol.47
, pp. 207-214
-
-
Hong, L.1
Lei, J.2
-
68
-
-
0029095929
-
Characterization of Langmuir-Blodgett flms of rhodopsin: Thermal stability studies
-
Maxia L, Radicchi G, Pepe IM, Nicolini C. Characterization of Langmuir-Blodgett flms of rhodopsin: thermal stability studies. Biophys J. 1995 Oct;69(4):1440–6.
-
(1995)
Biophys J
, vol.69
, Issue.4
, pp. 1440-1446
-
-
Maxia, L.1
Radicchi, G.2
Pepe, I.M.3
Nicolini, C.4
-
69
-
-
0027372021
-
Thermal stability of protein secondary structure in Lang-muir-Blodgett flms
-
Nicolini C, Erokhin V, Antolini F, Catasti P, Facci P. Thermal stability of protein secondary structure in Lang-muir-Blodgett flms. Biochim Biophys Acta. 1993 Nov 28;1158(3):273–8.
-
(1993)
Biochim Biophys Acta
, vol.1158
, Issue.3
, pp. 273-278
-
-
Nicolini, C.1
Erokhin, V.2
Antolini, F.3
Catasti, P.4
Facci, P.5
-
70
-
-
33144483698
-
Structure and growth of ul-trasmall protein microcrystals by synchrotron radiation: I. microGISAXS and microdiffraction of P450scc
-
Feb 15
-
Nicolini C, Pechkova E. Structure and growth of ul-trasmall protein microcrystals by synchrotron radiation: I. microGISAXS and microdiffraction of P450scc. J Cell Biochem. 2006 Feb 15;97(3):544–52.
-
(2006)
J Cell Biochem
, vol.97
, Issue.3
, pp. 544-552
-
-
Nicolini, C.1
Pechkova, E.2
-
71
-
-
33144473273
-
Structure and growth of ul-trasmall protein microcrystals by synchrotron radiation: II. microGISAX and microscopy of lysozyme
-
Feb 15
-
Pechkova E, Nicolini C. Structure and growth of ul-trasmall protein microcrystals by synchrotron radiation: II. microGISAX and microscopy of lysozyme. J Cell Biochem. 2006 Feb 15;97(3):553–60.
-
(2006)
J Cell Biochem
, vol.97
, Issue.3
, pp. 553-560
-
-
Pechkova, E.1
Nicolini, C.2
-
72
-
-
33144456311
-
Nicolini C. microGISAXS and protein nanotemplate crystallization: Methods and instrumentation
-
Nov
-
Pechkova E, Roth SV, Burghammer M, Fontani D, Riekel C, Nicolini C. microGISAXS and protein nanotemplate crystallization: methods and instrumentation. J Synchrotron Radiat. 2005 Nov;12(6):713–6.
-
(2005)
J Synchrotron Radiat
, vol.12
, Issue.6
, pp. 713-716
-
-
Pechkova, E.1
Roth, S.V.2
Burghammer, M.3
Fontani, D.4
Riekel, C.5
-
73
-
-
65549136743
-
MicroGISAXS of Langmuir-Blodgett protein flms: Effect of temperature on long-range order
-
May
-
Pechkova E, Tripathi S, Nicolini C. MicroGISAXS of Langmuir-Blodgett protein flms: effect of temperature on long-range order. J Synchrotron Radiat. 2009 May;16(3):330–5.
-
(2009)
J Synchrotron Radiat
, vol.16
, Issue.3
, pp. 330-335
-
-
Pechkova, E.1
Tripathi, S.2
Nicolini, C.3
-
74
-
-
79951931342
-
In situ study of nanotem-plate-induced growth of lysozyme microcrystals by submicrometer GISAXS
-
Mar
-
Pechkova E, Nicolini C. In situ study of nanotem-plate-induced growth of lysozyme microcrystals by submicrometer GISAXS. J Synchrotron Radiat. 2011 Mar;18(2):287-92.
-
(2011)
J Synchrotron Radiat
, vol.18
, Issue.2
, pp. 287-292
-
-
Pechkova, E.1
Nicolini, C.2
-
75
-
-
84894518764
-
Ab initio semi-quantitative analysis of micro-beam grazing-incidence small-angle x-ray scattering (M-GISAXS) during protein crystal nucleation and growth
-
Nicolini C, Bragazzi NL, Pechkova E, Lazzari R. Ab initio semi-quantitative analysis of micro-beam grazing-incidence small-angle x-ray scattering (M-GISAXS) during protein crystal nucleation and growth. J Proteomics Bioinform. 2014;7:064-070.
-
(2014)
J Proteomics Bioinform
, vol.7
, pp. 064-070
-
-
Nicolini, C.1
Bragazzi, N.L.2
Pechkova, E.3
Lazzari, R.4
-
76
-
-
34548633585
-
Protein thermal stability: The role of protein structure and aqueous environment
-
Oct 1
-
Pechkova E, Sivozhelezov V, Nicolini C. Protein thermal stability: the role of protein structure and aqueous environment. Arch Biochem Biophys. 2007 Oct 1;466(1):40–8.
-
(2007)
Arch Biochem Biophys
, vol.466
, Issue.1
, pp. 40-48
-
-
Pechkova, E.1
Sivozhelezov, V.2
Nicolini, C.3
|