Inhibition of human α-thrombin by a phosphonate tripeptide proceeds via a metastable pentacoordinated phosphorus intermediate 1 1Edited by R. Huber

Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry

“…The coordinates of human thrombin (PDB code 1H8D) 29 were used for initial rigid body refinement of the protein molecules followed by repeated cycles of conjugate gradient energy minimization, simulated annealing and B-factor refinement using the CNS program package. 30 Table 3.…”

Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin

“…The coordinates of human thrombin (PDB code 1H8D) 36 were used for initial rigid-body refinement of the protein molecules followed by repeated cycles of maximum likelihood energy minimization, simulated annealing, and B-factor refinement using the CNS program package. 37 Refinement of structure 2 was done with SHELXL, 38 and structures 3, 4, 5, 6, 7, 8, 9, 10, and 11 were refined with PHENIX.…”

Think Twice: Understanding the High Potency of Bis(phenyl)methane Inhibitors of Thrombin

“…The coordinates of human thrombin (PDB code 1H8D) 22 were used for initial rigid-body refinement of the protein molecules, followed by repeated cycles of conjugate gradient energy minimisation, simulated annealing and B-factor refinement using the CNS program package. 23 Refinement at later stages was performed with the program SHELXL.…”