dynamics studies of proteins. J Phys Chem B
102(18):3586–3616
25. Landau M, Mayrose I, Rosenberg Y, Glaser F,
Martz E, Pupko T, Ben-Tal N (2005) ConSurf
2005: the projection of evolutionary conservation scores of residues on protein structures.
Nucleic Acids Res 33(suppl 2):W299–W302
26. Katoh K, Misawa K, Ki K, Miyata T (2002)
MAFFT: a novel method for rapid multiple
sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066
27. Ichiye T, Karplus M (1991) Collective
motions in proteins: a covariance analysis of
atomic fluctuations in molecular dynamics
and normal mode simulations. Proteins 11
(3):205–217
28. Glykos NM (2006) Software news and updates
carma: a molecular dynamics analysis program.
J Comput Chem 27(14):1765–1768
29. Girvan M, Newman ME (2002) Community
structure in social and biological networks.
Proc Natl Acad Sci 99(12):7821–7826
30. Eargle J, Luthey-Schulten Z (2012) NetworkView: 3D display and analysis of protein· RNA
interaction networks. Bioinformatics 28
(22):3000–3001
The Allosteric Effect in Antibody-Antigen Recognition
183
102(18):3586–3616
25. Landau M, Mayrose I, Rosenberg Y, Glaser F,
Martz E, Pupko T, Ben-Tal N (2005) ConSurf
2005: the projection of evolutionary conservation scores of residues on protein structures.
Nucleic Acids Res 33(suppl 2):W299–W302
26. Katoh K, Misawa K, Ki K, Miyata T (2002)
MAFFT: a novel method for rapid multiple
sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066
27. Ichiye T, Karplus M (1991) Collective
motions in proteins: a covariance analysis of
atomic fluctuations in molecular dynamics
and normal mode simulations. Proteins 11
(3):205–217
28. Glykos NM (2006) Software news and updates
carma: a molecular dynamics analysis program.
J Comput Chem 27(14):1765–1768
29. Girvan M, Newman ME (2002) Community
structure in social and biological networks.
Proc Natl Acad Sci 99(12):7821–7826
30. Eargle J, Luthey-Schulten Z (2012) NetworkView: 3D display and analysis of protein· RNA
interaction networks. Bioinformatics 28
(22):3000–3001
The Allosteric Effect in Antibody-Antigen Recognition
183
