Biology Reference
In-Depth Information
52. Moreira IS, Fernandes PA, Ramos MJ. (2007). Computational alanine scanning
mutagenesis — an improved methodological approach
. J Comput Chem
28
:
644-54.
53. Rizzo RC, Toba S, Kuntz ID. (2004) A molecular basis for the selectivity of thia-
diazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized
Born molecular dynamics simulations
. J Med Chem
47
: 3065-74.
54. Pearlman DA. (2005) Evaluating the molecular mechanics Poisson-Boltzmann
surface area free energy method using a congeneric series of ligands to p38 MAP
kinase
. J Med Chem
48
: 7796-807.
55. Foloppe N, Hubbard R. (2006) Towards predictive ligand design with free-
energy based computational methods?
Curr Med Chem
13
: 3583-608.
56. Kuhn B, Gerber P, Schulz-Gasch T, Stahl M. (2005) Validation and use of the
MM-PBSA approach for drug discovery
. J Med Chem
48
: 4040-8.
57. Huo S, Massova I, Kollman PA. (2002) Computational alanine scanning of the
1: 1 human growth hormone-receptor complex
. J Comput Chem
23
: 15-27.
58. Massova I, Kollman PA. (1999) Computational alanine scanning to probe protein-
protein interactions: a novel approach to evaluate binding free energies
.
J Am Chem Soc
121
: 8133-43.
59. 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
67
: 1026-47.
60. Lafont V, Schaefer M, Stote RH
et al
. (2007) Protein-protein recognition and
interaction hot spots in an antigen-antibody complex: free energy decomposi-
tion identifies “efficient amino acids”
. Proteins
67
: 418-34.
61. Zoete V, Meuwly M. (2006) Importance of individual side chains for the stability
of a protein fold: computational alanine scanning of the insulin monomer
.
J Comput Chem
27
: 1843-57.
62. Yip YL, Zoete V, Scheib H, Michielin O. (2006) Structural assessment of single
amino acid mutations: application to TP53 function
. Hum Mutat
27
: 926-37.
63. Michalik L, Zoete V, Krey G
et al
. (2007) Combined simulation and mutagenesis
analyses reveal the involvement of key residues for peroxisome proliferator-
activated receptor alpha helix 12 dynamic behavior
. J Biol Chem
282
: 9666-77.
64. Sono M, Roach MP, Coulter ED, Dawson JH. (1996) Heme-containing
oxygenases
. Chem Rev
96
: 2841-88.
65. Uyttenhove C, Pilotte L, Theate I
et al
. (2003) Evidence for a tumoral immune
resistance mechanism based on tryptophan degradation by indoleamine
2,3-dioxygenase
. Nat Med
9
: 1269-74.
66. Muller AJ, DuHadaway JB, Donover PS
et al
. (2005). Inhibition of indoleamine
2,3-dioxygenase, an immunoregulatory target of the cancer suppression gene
Bin1, potentiates cancer chemotherapy
. Nat Med
11
: 312-9.
