-
1
-
-
0003880161
-
-
(4th ed.). New York: Garland Science
-
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walters, P. (Eds.). (2002). Molecular biology of the cell (4th ed.). New York: Garland Science.
-
(2002)
Molecular biology of the cell
-
-
Alberts, B.1
Johnson, A.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Walters, P.6
-
2
-
-
32544458887
-
T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3D structure-DB
-
Kaas, Q., & Lefranc, M. P. (2005). T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3D structure-DB. In Silico Biology, 5, 505-528.
-
(2005)
In Silico Biology
, vol.5
, pp. 505-528
-
-
Kaas, Q.1
Lefranc, M.P.2
-
3
-
-
42649112362
-
Evolutionarily conserved amino acids that control TCR-MHC interaction
-
Marrack, P., Scott-Browne, J. P., Dai, S., Gapin, L., & Kappler, J. W. (2008). Evolutionarily conserved amino acids that control TCR-MHC interaction. Annual Reviews in Immunology, 26, 171-203.
-
(2008)
Annual Reviews in Immunology
, vol.26
, pp. 171-203
-
-
Marrack, P.1
Scott-Browne, J.P.2
Dai, S.3
Gapin, L.4
Kappler, J.W.5
-
4
-
-
47649130715
-
Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities
-
Armstrong, K. M., Insaidoo, F. K., & Baker, B. M. (2008). Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities. Journal of Molecular Recognition, 21, 275-287.
-
(2008)
Journal of Molecular Recognition
, vol.21
, pp. 275-287
-
-
Armstrong, K.M.1
Insaidoo, F.K.2
Baker, B.M.3
-
5
-
-
58149280299
-
T-cell receptor binding affinities and kinetics: Impact on T-cell activity and specificity
-
Stone, J. D., Chervin, A. S., & Kranz, D. M. (2009). T-cell receptor binding affinities and kinetics: Impact on T-cell activity and specificity. Immunology, 126, 165-176.
-
(2009)
Immunology
, vol.126
, pp. 165-176
-
-
Stone, J.D.1
Chervin, A.S.2
Kranz, D.M.3
-
6
-
-
0033118739
-
A kinetic basis for T cell receptor repertoire selection during an immune response
-
Savage, P. A., Boniface, J. J., & Davis, M. M. (1999). A kinetic basis for T cell receptor repertoire selection during an immune response. Immunity, 10, 485-492.
-
(1999)
Immunity
, vol.10
, pp. 485-492
-
-
Savage, P.A.1
Boniface, J.J.2
Davis, M.M.3
-
7
-
-
0031172162
-
Serial triggering of TCRs: A basis for the sensitivity and specificity of antigen recognition
-
Valitutti, S., & Lanzavecchia, A. (1997). Serial triggering of TCRs: A basis for the sensitivity and specificity of antigen recognition. Immunology Today, 18, 299-304.
-
(1997)
Immunology Today
, vol.18
, pp. 299-304
-
-
Valitutti, S.1
Lanzavecchia, A.2
-
8
-
-
0348047600
-
Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation
-
Krogsgaard, M., Prado, N., Adams, E. J., He, X., Chow, D. C., Wilson, D. B., et al. (2003). Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation. Molecular Cell, 12, 1367-1378.
-
(2003)
Molecular Cell
, vol.12
, pp. 1367-1378
-
-
Krogsgaard, M.1
Prado, N.2
Adams, E.J.3
He, X.4
Chow, D.C.5
Wilson, D.B.6
Garcia, K.C.7
Davis, M.M.8
-
9
-
-
71749112218
-
T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility
-
Borbulevych, O. Y., Piepenbrink, K. H., Gloor, B. E., Scott, D. R., Sommese, R. F., Cole, D. K., et al. (2009). T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity, 31, 885-896.
-
(2009)
Immunity
, vol.31
, pp. 885-896
-
-
Borbulevych, O.Y.1
Piepenbrink, K.H.2
Gloor, B.E.3
Scott, D.R.4
Sommese, R.F.5
Cole, D.K.6
Sewell, A.K.7
Baker, B.M.8
-
10
-
-
34247346627
-
How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?
-
Mazza, C., Auphan-Anezin, N., Gregoire, C., Guimezanes, A., Kellenberger, C., Roussel, A., et al. (2007). How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides? The EMBO Journal, 26, 1972-1983.
-
(2007)
The EMBO Journal
, vol.26
, pp. 1972-1983
-
-
Mazza, C.1
Auphan-Anezin, N.2
Gregoire, C.3
Guimezanes, A.4
Kellenberger, C.5
Roussel, A.6
Kearney, A.7
van der Merwe, P.8
Schmitt-Verhulst, A.M.9
Malissen, B.10
-
11
-
-
0036536428
-
Molecular dynamics simulations
-
Hansson, T., Oostenbrink, C., & van Gunsteren, W. F. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12, 190-196.
-
(2002)
Current Opinion in Structural Biology
, vol.12
, pp. 190-196
-
-
Hansson, T.1
Oostenbrink, C.2
van Gunsteren, W.F.3
-
12
-
-
0037343308
-
Molecular dynamics of biological macromolecules: A brief history and perspective
-
Karplus, M. (2003). Molecular dynamics of biological macromolecules: A brief history and perspective. Biopolymers, 68, 350-358.
-
(2003)
Biopolymers
, vol.68
, pp. 350-358
-
-
Karplus, M.1
-
13
-
-
39449116285
-
Biomolecular simulation: historical picture and future perspectives
-
van Gunsteren, W. F., & Dolenc, J. (2008). Biomolecular simulation: historical picture and future perspectives. Biochemical Society Transactions, 36, 11-15.
-
(2008)
Biochemical Society Transactions
, vol.36
, pp. 11-15
-
-
van Gunsteren, W.F.1
Dolenc, J.2
-
14
-
-
58149292269
-
Computer modeling in biotechnology: A partner in development
-
Aksimentiev, A., Brunner, R., Cohen, J., Comer, J., Cruz-Chu, E., Hardy, D., et al. (2008). Computer modeling in biotechnology: A partner in development. Methods in Molecular Biology, 474, 181-234.
-
(2008)
Methods in Molecular Biology
, vol.474
, pp. 181-234
-
-
Aksimentiev, A.1
Brunner, R.2
Cohen, J.3
Comer, J.4
Cruz-Chu, E.5
Hardy, D.6
Rajan, A.7
Shih, A.8
Sigalov, G.9
Yin, Y.10
Schulten, K.11
-
15
-
-
64049102289
-
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get"
-
Mobley, D. L., & Dill, K. A. (2009). Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure, 17, 489-499.
-
(2009)
Structure
, vol.17
, pp. 489-499
-
-
Mobley, D.L.1
Dill, K.A.2
-
16
-
-
41949112774
-
Molecular simulation as an aid to experimentalists
-
van Gunsteren, W. F., Dolenc, J., & Mark, A. E. (2008). Molecular simulation as an aid to experimentalists. Current Opinion in Structural Biology, 18, 149-153.
-
(2008)
Current Opinion in Structural Biology
, vol.18
, pp. 149-153
-
-
van Gunsteren, W.F.1
Dolenc, J.2
Mark, A.E.3
-
17
-
-
34248358109
-
Applications of Molecular Dynamics Simulations in immunology: A useful computational method in aiding vaccine design
-
Mallik, B., & Morikis, D. (2006). Applications of Molecular Dynamics Simulations in immunology: A useful computational method in aiding vaccine design. Current Proteomics, 3, 259-270.
-
(2006)
Current Proteomics
, vol.3
, pp. 259-270
-
-
Mallik, B.1
Morikis, D.2
-
18
-
-
0036447407
-
Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis
-
Michielin, O., & Karplus, M. (2002). Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. Journal of Molecular Biology, 324, 547-569.
-
(2002)
Journal of Molecular Biology
, vol.324
, pp. 547-569
-
-
Michielin, O.1
Karplus, M.2
-
19
-
-
7644220670
-
Physical methods for structure, dynamics and binding in immunological research
-
Morikis, D., & Lambris, J. D. (2004). Physical methods for structure, dynamics and binding in immunological research. Trends in Immunology, 25, 700-707.
-
(2004)
Trends in Immunology
, vol.25
, pp. 700-707
-
-
Morikis, D.1
Lambris, J.D.2
-
20
-
-
58549110833
-
A disulfide linked model of the complement protein C8γ complexed with C8α indel peptide
-
Stavrakoudis, A. (2009). A disulfide linked model of the complement protein C8γ complexed with C8α indel peptide. Journal of Molecular Modeling, 15, 165-171.
-
(2009)
Journal of Molecular Modeling
, vol.15
, pp. 165-171
-
-
Stavrakoudis, A.1
-
21
-
-
78049512800
-
Conformational flexibility in designing peptides for immunology: The molecular dynamics approach
-
Stavrakoudis, A. (2010). Conformational flexibility in designing peptides for immunology: The molecular dynamics approach. Current Computer-Aided Drug Design, 6, 207-222.
-
(2010)
Current Computer-Aided Drug Design
, vol.6
, pp. 207-222
-
-
Stavrakoudis, A.1
-
22
-
-
37349112664
-
Toward an atomistic understanding of the immune synapse: large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex
-
Wan, S., Flower, D. R., & Coveney, P. V. (2008). Toward an atomistic understanding of the immune synapse: large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex. Molecular Immunology, 45, 1221-1230.
-
(2008)
Molecular Immunology
, vol.45
, pp. 1221-1230
-
-
Wan, S.1
Flower, D.R.2
Coveney, P.V.3
-
23
-
-
78149316174
-
T-cell epitope prediction and immune complex simulation using molecular dynamics: State of the art and persisting challenges
-
doi:10.1186/1745-7580-6-S2-S4
-
Flower, D. R., Phadwal, K., Macdonald, I. K., Coveney, P., Davies, M. N., & Wan, S. (2010). T-cell epitope prediction and immune complex simulation using molecular dynamics: State of the art and persisting challenges. Immunome Research, 6(Suppl 2), S4. doi: 10. 1186/1745-7580-6-S2-S4.
-
(2010)
Immunome Research
, vol.6
, Issue.SUPPL. 2
-
-
Flower, D.R.1
Phadwal, K.2
Macdonald, I.K.3
Coveney, P.4
Davies, M.N.5
Wan, S.6
-
24
-
-
48349146758
-
Patient-specific simulation as a basis for clinical decision-making
-
Sadiq, S. K., Mazzeo, M. D., Zasada, S. J., Manos, S., Stoica, I., Gale, C. V., et al. (2008). Patient-specific simulation as a basis for clinical decision-making. Philosophical Transactions of the Royal Society A, 366, 3199-3219.
-
(2008)
Philosophical Transactions of the Royal Society A
, vol.366
, pp. 3199-3219
-
-
Sadiq, S.K.1
Mazzeo, M.D.2
Zasada, S.J.3
Manos, S.4
Stoica, I.5
Gale, C.V.6
Watson, S.J.7
Kellam, P.8
Brew, S.9
Coveney, P.V.10
-
25
-
-
56049117665
-
Protein-protein interaction investigated by steered molecular dynamics: The TCR-pMHC complex
-
Cuendet, M. A., & Michielin, O. (2008). Protein-protein interaction investigated by steered molecular dynamics: The TCR-pMHC complex. Biophysical Journal, 95, 3575-3590.
-
(2008)
Biophysical Journal
, vol.95
, pp. 3575-3590
-
-
Cuendet, M.A.1
Michielin, O.2
-
26
-
-
22544456941
-
Peptide recognition by the T cell receptor: Comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
-
Wan, S., Coveney, P. V., & Flower, D. R. (2005). Peptide recognition by the T cell receptor: Comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations. Philosophical Transactions of the Royal Society A, 363, 2037-2053.
-
(2005)
Philosophical Transactions of the Royal Society A
, vol.363
, pp. 2037-2053
-
-
Wan, S.1
Coveney, P.V.2
Flower, D.R.3
-
27
-
-
34248562740
-
comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: Application to the TCR-p-MHC complex
-
Zoete, V., & Michielin, O. (2007). comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: Application to the TCR-p-MHC complex. Proteins: Structure, Function, and Bioinformatics, 67, 1026-1047.
-
(2007)
Proteins: Structure, Function, and Bioinformatics
, vol.67
, pp. 1026-1047
-
-
Zoete, V.1
Michielin, O.2
-
28
-
-
76649121529
-
MM-GBSA binding free energy decomposition and T cell receptor engineering
-
Zoete, V., Irving, M. B., & Michielin, O. (2009). MM-GBSA binding free energy decomposition and T cell receptor engineering. Journal of Molecular Recognition, 23, 142-152.
-
(2009)
Journal of Molecular Recognition
, vol.23
, pp. 142-152
-
-
Zoete, V.1
Irving, M.B.2
Michielin, O.3
-
29
-
-
0037240790
-
A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity
-
Kjer-Nielsen, L., Clements, C. S., Purcell, A. W., Brooks, A. G., Whisstock, J. C., Burrows, S. R., et al. (2003). A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity. Immunity, 18, 53-64.
-
(2003)
Immunity
, vol.18
, pp. 53-64
-
-
Kjer-Nielsen, L.1
Clements, C.S.2
Purcell, A.W.3
Brooks, A.G.4
Whisstock, J.C.5
Burrows, S.R.6
McCluskey, J.7
Rossjohn, J.8
-
30
-
-
59449097827
-
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions
-
Koch, O., & Klebe, G. (2009). Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions. Proteins: Structure, Function, and Bioinformatics, 74, 353-357.
-
(2009)
Proteins: Structure, Function, and Bioinformatics
, vol.74
, pp. 353-357
-
-
Koch, O.1
Klebe, G.2
-
31
-
-
0036616218
-
The protein data bank
-
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., et al. (2002). The protein data bank. Acta Crystallographica Section D, 58, 899-907.
-
(2002)
Acta Crystallographica Section D
, vol.58
, pp. 899-907
-
-
Berman, H.M.1
Battistuz, T.2
Bhat, T.N.3
Bluhm, W.F.4
Bourne, P.E.5
Burkhardt, K.6
Feng, Z.7
Gilliland, G.L.8
Iype, L.9
Jain, S.10
Fagan, P.11
Marvin, J.12
Padilla, D.13
Ravichandran, V.14
Schneider, B.15
Thanki, N.16
Weissig, H.17
Westbrook, J.D.18
Zardecki, C.19
-
32
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33-38.
-
(1996)
Journal of Molecular Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
33
-
-
0034250744
-
An improved empirical potential energy function for molecular simulations of phospholipids
-
Feller, S. E., & MacKerell, A. D., Jr. (2000). An improved empirical potential energy function for molecular simulations of phospholipids. The Journal of Physical Chemistry B, 104, 7510-7515.
-
(2000)
The Journal of Physical Chemistry B
, vol.104
, pp. 7510-7515
-
-
Feller, S.E.1
Mackerell Jr., A.D.2
-
34
-
-
0033614004
-
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word, J. M., Lovell, S. C., Richardson, J. S., & Richardson, D. C. (1999). Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Journal of Molecular Biology, 285, 1735-1747.
-
(1999)
Journal of Molecular Biology
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
35
-
-
0035526029
-
Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
-
Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105, 9954-9960.
-
(2001)
The Journal of Physical Chemistry A
, vol.105
, pp. 9954-9960
-
-
Mark, P.1
Nilsson, L.2
-
36
-
-
0343005873
-
Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation
-
Weber, W., Hunenberger, P. H., & McCammon, J. A. (2000). Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. The Journal of Physical Chemistry B, 104, 3668-3675.
-
(2000)
The Journal of Physical Chemistry B
, vol.104
, pp. 3668-3675
-
-
Weber, W.1
Hunenberger, P.H.2
McCammon, J.A.3
-
37
-
-
33846823909
-
Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
-
Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 10089-11092.
-
(1993)
Journal of Chemical Physics
, vol.98
, pp. 10089-11092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
38
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327-341.
-
(1977)
Journal of Computational Physics
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
39
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller, S. E., Zhang, Y., Pastor, R. W., & Brooks, B. R. (1995). Constant pressure molecular dynamics simulation: The Langevin piston method. The Journal of Physical Chemistry B, 103, 4613-4621.
-
(1995)
The Journal of Physical Chemistry B
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
40
-
-
78650722548
-
Eucb: A C++ program for molecular dynamics trajectory analysis
-
Tsoulos, I. G., & Stavrakoudis, A. (2011). Eucb: A C++ program for molecular dynamics trajectory analysis. Computer Physics Communications, 182, 834-841.
-
(2011)
Computer Physics Communications
, vol.182
, pp. 834-841
-
-
Tsoulos, I.G.1
Stavrakoudis, A.2
-
41
-
-
0345280708
-
Determination of mean and standard deviation of dihedral angles
-
Döker, R., Maurer, T., Kremer, W., Neidig, K., & Kalbitzer, H. R. (1999). Determination of mean and standard deviation of dihedral angles. Biochemical and Biophysical Research Communications, 257, 348-350.
-
(1999)
Biochemical and Biophysical Research Communications
, vol.257
, pp. 348-350
-
-
Döker, R.1
Maurer, T.2
Kremer, W.3
Neidig, K.4
Kalbitzer, H.R.5
-
42
-
-
0021203270
-
A comparison of several "single-pass" estimators of the standard deviation of wind direction
-
Yamartino, R. J. (1984). A comparison of several "single-pass" estimators of the standard deviation of wind direction. Journal of Climate and Applied Meteorology, 23, 1362-1366.
-
(1984)
Journal of Climate and Applied Meteorology
, vol.23
, pp. 1362-1366
-
-
Yamartino, R.J.1
-
43
-
-
0028566270
-
A revised set of potentials for beta-turn formation in proteins
-
Hutchinson, E. G., & Thornton, J. M. (1994). A revised set of potentials for beta-turn formation in proteins. Protein Science, 3, 2207-22016.
-
(1994)
Protein Science
, vol.3
, pp. 2207-22016
-
-
Hutchinson, E.G.1
Thornton, J.M.2
-
44
-
-
0024279235
-
Analysis and prediction of the different types of β-turn in proteins
-
Wilmot, C. M., & Thornton, J. M. (1988). Analysis and prediction of the different types of β-turn in proteins. Journal of Molecular Biology, 203, 221-232.
-
(1988)
Journal of Molecular Biology
, vol.203
, pp. 221-232
-
-
Wilmot, C.M.1
Thornton, J.M.2
-
45
-
-
33749172039
-
Carma: A molecular dynamics analysis program
-
Glykos, N. M. (2006). Carma: A molecular dynamics analysis program. Journal of Computational Chemistry, 27, 1765-1768.
-
(2006)
Journal of Computational Chemistry
, vol.27
, pp. 1765-1768
-
-
Glykos, N.M.1
-
47
-
-
0001351515
-
Estimation of absolute and relative entropies of macromolecules using the covariance matrix
-
Schlitter, J. (1993). Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chemical Physics Letters, 215, 617-621.
-
(1993)
Chemical Physics Letters
, vol.215
, pp. 617-621
-
-
Schlitter, J.1
-
48
-
-
0035828630
-
On the calculation of entropy from covariance matrices of the atomic fluctuations
-
Andricioaei, I., & Karplus, M. (2001). On the calculation of entropy from covariance matrices of the atomic fluctuations. The Journal of Chemical Physics, 115, 6289.
-
(2001)
The Journal of Chemical Physics
, vol.115
, pp. 6289
-
-
Andricioaei, I.1
Karplus, M.2
-
49
-
-
33645786604
-
Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme
-
Buck, M., Bouguet-Bonnet, S., Pastor, R. W., & MacKerell, A. D., Jr. (2006). Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme. Biophysical Journal, 90, 36-38.
-
(2006)
Biophysical Journal
, vol.90
, pp. 36-38
-
-
Buck, M.1
Bouguet-Bonnet, S.2
Pastor, R.W.3
Mackerell Jr., A.D.4
-
50
-
-
48749111845
-
Molecular dynamics simulations of an apoliprotein derived peptide
-
Stavrakoudis, A. (2008). Molecular dynamics simulations of an apoliprotein derived peptide. Chemical Physics Letters, 461, 294-299.
-
(2008)
Chemical Physics Letters
, vol.461
, pp. 294-299
-
-
Stavrakoudis, A.1
-
51
-
-
10844292652
-
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
-
Mu, Y., Nguyen, P. H., & Stock, G. (2005). Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins: Structure, Function, and Bioinformatics, 58, 45-52.
-
(2005)
Proteins: Structure, Function, and Bioinformatics
, vol.58
, pp. 45-52
-
-
Mu, Y.1
Nguyen, P.H.2
Stock, G.3
-
52
-
-
73949118375
-
Molecular Dynamics simulations of BcZBP, a deacetylase from bacillus cereus: active site loops determine substrate accessibility and specificity
-
Fadouloglou, V. E., Stavrakoudis, A., Bouriotis, V., Kokkinidis, M., & Glykos, N. M. (2009). Molecular Dynamics simulations of BcZBP, a deacetylase from bacillus cereus: active site loops determine substrate accessibility and specificity. The Journal of Chemical Theory and Computation, 5, 3299-3311.
-
(2009)
The Journal of Chemical Theory and Computation
, vol.5
, pp. 3299-3311
-
-
Fadouloglou, V.E.1
Stavrakoudis, A.2
Bouriotis, V.3
Kokkinidis, M.4
Glykos, N.M.5
-
53
-
-
40849101548
-
Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors
-
Hoare, H. L., Sullivan, L. C., Clements, C. S., Ely, L. K., Beddoe, T., Henderson, K., et al. (2008). Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors. Journal of Molecular Biology, 377, 1297-1303.
-
(2008)
Journal of Molecular Biology
, vol.377
, pp. 1297-1303
-
-
Hoare, H.L.1
Sullivan, L.C.2
Clements, C.S.3
Ely, L.K.4
Beddoe, T.5
Henderson, K.6
Lin, J.7
Reid, H.8
Brooks, A.9
Rossjohn, J.10
-
54
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman, D., & Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins: Structure, Function and Genetics, 23, 566-579.
-
(1995)
Proteins: Structure, Function and Genetics
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
55
-
-
23244438846
-
Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression
-
Stewart-Jones, G. B., Gillespie, G., Overton, I. M., Kaul, R., Roche, P., McMichael, A. J., et al. (2005). Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression. Journal of Immunology, 175, 2459-2468.
-
(2005)
Journal of Immunology
, vol.175
, pp. 2459-2468
-
-
Stewart-Jones, G.B.1
Gillespie, G.2
Overton, I.M.3
Kaul, R.4
Roche, P.5
McMichael, A.J.6
Rowland-Jones, S.7
Jones, E.Y.8
-
56
-
-
60549093248
-
Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition
-
Archbold, J. K., Macdonald, W. A., Gras, S., Ely, L. K., Miles, J. J., Bell, M. J., et al. (2009). Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition. Journal of Experimental Medicine, 206, 209-219.
-
(2009)
Journal of Experimental Medicine
, vol.206
, pp. 209-219
-
-
Archbold, J.K.1
Macdonald, W.A.2
Gras, S.3
Ely, L.K.4
Miles, J.J.5
Bell, M.J.6
Brennan, R.M.7
Beddoe, T.8
Wilce, M.C.J.9
Clements, C.S.10
Purcell, A.W.11
McCluskey, J.12
Burrows, S.R.13
Rossjohn, J.14
-
57
-
-
58849111704
-
Molecular dynamics simulations of the TSSPSAD Peptide Antigen in free and bound with CAMPATH-1H Fab antibody states: the importance of the β-turn conformation
-
Tatsis, V. A., Tsoulos, I. G., & Stavrakoudis, A. (2009). Molecular dynamics simulations of the TSSPSAD Peptide Antigen in free and bound with CAMPATH-1H Fab antibody states: the importance of the β-turn conformation. International Journal of Peptide Research and Therapeutics, 15, 1-9.
-
(2009)
International Journal of Peptide Research and Therapeutics
, vol.15
, pp. 1-9
-
-
Tatsis, V.A.1
Tsoulos, I.G.2
Stavrakoudis, A.3
-
58
-
-
34249061686
-
On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement
-
Glykos, N. (2007). On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement. Acta Crystallographica Section D, D63, 705-713.
-
(2007)
Acta Crystallographica Section D
, vol.D63
, pp. 705-713
-
-
Glykos, N.1
-
59
-
-
0030961098
-
Backbone entropy of loops as a measure of their flexibility: application to a ras protein simulated by molecular dynamics
-
Meirovitch, H., & Hendrickson, T. F. (1997). Backbone entropy of loops as a measure of their flexibility: application to a ras protein simulated by molecular dynamics. Proteins: Structure, Function, and Bioinformatics, 29, 127-140.
-
(1997)
Proteins: Structure, Function, and Bioinformatics
, vol.29
, pp. 127-140
-
-
Meirovitch, H.1
Hendrickson, T.F.2
-
60
-
-
54049111388
-
Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes
-
Armstrong, K. M., Piepenbrink, K. H., & Baker, B. M. (2008). Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochemical Journal, 415, 183-196.
-
(2008)
Biochemical Journal
, vol.415
, pp. 183-196
-
-
Armstrong, K.M.1
Piepenbrink, K.H.2
Baker, B.M.3
-
61
-
-
0036839356
-
The structure of HLA-B8 complexed to an immunodominant viral determinant: Peptide-induced conformational changes and a mode of MHC class I dimerization
-
Kjer-Nielsen, L., Clements, C. S., Brooks, A. G., Purcell, A. W., Fontes, M., McCluskey, J., et al. (2002). The structure of HLA-B8 complexed to an immunodominant viral determinant: Peptide-induced conformational changes and a mode of MHC class I dimerization. The Journal of Immunology, 169, 5153-5160.
-
(2002)
The Journal of Immunology
, vol.169
, pp. 5153-5160
-
-
Kjer-Nielsen, L.1
Clements, C.S.2
Brooks, A.G.3
Purcell, A.W.4
Fontes, M.5
McCluskey, J.6
Rossjohn, J.7
-
62
-
-
38949100462
-
The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vβ domain
-
Ishizuka, J., Stewart-Jones, G. B. E., van der Merwe, A., Bell, J. I., McMichael, A. J., & Jones, E. Y. (2008). The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vβ domain. Immunity, 28, 171-182.
-
(2008)
Immunity
, vol.28
, pp. 171-182
-
-
Ishizuka, J.1
Stewart-Jones, G.B.E.2
van der Merwe, A.3
Bell, J.I.4
McMichael, A.J.5
Jones, E.Y.6
-
64
-
-
1842534583
-
MHC-peptide binding is assisted by bound water molecules
-
Petrone, P. M., & Garcia, A. E. (2004). MHC-peptide binding is assisted by bound water molecules. Journal of Molecular Biology, 338, 419-435.
-
(2004)
Journal of Molecular Biology
, vol.338
, pp. 419-435
-
-
Petrone, P.M.1
Garcia, A.E.2
-
65
-
-
0021470624
-
Buried surface area conformational entropy, and protein stability
-
Rashin, A. (1984). Buried surface area conformational entropy, and protein stability. Biopolymers, 23, 1605-1620.
-
(1984)
Biopolymers
, vol.23
, pp. 1605-1620
-
-
Rashin, A.1
-
66
-
-
65249187243
-
MM-PBSA captures key role of intercalating water molecules at a protein-protein interface
-
Wong, S., Amaro, R. E., & McCammon, J. A. (2009). MM-PBSA captures key role of intercalating water molecules at a protein-protein interface. The Journal of Chemical Theory and Computation, 5, 422-429.
-
(2009)
The Journal of Chemical Theory and Computation
, vol.5
, pp. 422-429
-
-
Wong, S.1
Amaro, R.E.2
McCammon, J.A.3
|