Primary Citation PubMed: 15858274
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Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces.
(2008) BMC Bioinformatics 9
PubMed: 18939984 | PubMedCentral: PMC2596146 | DOI: 10.1186/1471-2105-9-448
Protein A Protein B ΔG (kJ/mole) PDB Ref BPTI Chymotrypsin -44.96 1CBW [ 49 ] Barnase Barstar -79.50 1B27 [ 50 ] Subtilisin Carlsberg OMTKY3 -59.31 1R0R [ 51 ] Rap1A Raf1 -35.98 1C1Y [ 52 ] Ra... Byr2 -38.45 1K8R [ 53 ] Fv D1.3 Fv E5.2 -45.48 1DVF [ 54 ] Fv D1.3 HEWL -45.10 1VFB [ 55 ] BPTI Trypsin -75.16 2PTC [ 49 ] HyHEL10 Fab HEWL -56.21 3HFM [ 56 ] RalGDS Ras -35.15 1LFD [ 57 ] Subtilisin Carlsberg Eglin C -54.76 1CSE [ 58 ] IM9 Colicin E9 -78.62 1EMV [ 59 ] HyHEL5 Fab HEWL -59.36 1YQV [ 60 ] SGPB OMTKY3 -61.45 3SGB [ 61 ] Ribonuclease Inhibitor Angiogenin -87.15 1A4Y [ 62 ] N9 Neuraminidase NC10 Fab -48.50 1NMB [ 63 ] Subtilisin BPN' SSI -61.33 2SIC [ 64 ] Thrombin Thrombomodulin -53.09 1DX5 [ 65 ] Ribonuclease A Ribonuclease Inhibitor -76.30 1DFJ [ 62 ] Kallikrein A BPTI -51.83 2KAI [ 66 ] Protein constituents of the complexes are given, with the following abbreviations: OMTKY3, turkey ovomucoid third domain; HEWL, Hen Egg White Lysozyme; BPTI, Bovine Pancreatic Trypsin Inhibitor; IM9, Immunity Protein 9; SGPB Streptomyces griseus protease B; SSI, Streptomyces Subtilisin Inhibitor.
Publication Year: 2008
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.
(2012) Acta Crystallogr D Biol Crystallogr 68
PubMed: 22505258 | PubMedCentral: PMC3322597 | DOI: 10.1107/S0907444911047834
These test cases were PDB entries 2aea (2.58 Å)/ 2apj (1.6 Å), 1gtx (3.0 Å)/ 1ohv (2.3 Å) (see § 2.3.1), 3hfl (2.65 ... 0c5;)/ 1yqv (1.7 Å) and 4tsu (2.5 Å)/ 1oh0 (1.1 Å).
Publication Year: 2012
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