Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine

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Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1002/(SICI)1097-0134(19991201)37:4<641::AID-PROT14>3.0.CO;2-W
P698PubMed publication ID10651279

P2093author name stringA T Brunger
N Ota
S A Shah
M Mares-Guia
C Stroupe
J M Ferreira-da-Silva
P2860cites workStructure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution.Q52891962
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Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolutionQ36280516
Active site dynamics of ribonucleaseQ37539535
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
The refined crystal structure of bovine beta-trypsin at 1.8 A resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0Q39064701
Crystallographic and NMR studies of the serine proteasesQ40335461
Water: now you see it, now you don'tQ40700389
Electronic effects in the interaction of para-substituted benzamidines with trypsin: the involvement of the pi-electronic density at the central atom of the substituent in bindingQ44275374
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambinQ47682341
Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysisQ51197836
15N NMR spectroscopy of hydrogen-bonding interactions in the active site of serine proteases: evidence for a moving histidine mechanism.Q52493354
P433issue4
P407language of work or nameEnglishQ1860
P921main subjectmacromoleculeQ178593
P304page(s)641-53
P577publication date1999-12-01
P1433published inProteinsQ7251514
P1476titleNon-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine
P478volume37

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cites work (P2860)
Q43887767Agmatine oxidation by copper amine oxidase
Q36802557Application of a polarizable force field to calculations of relative protein-ligand binding affinities
Q41965796Conformational variability of benzamidinium-based inhibitors
Q34457491Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
Q84743382Quantifying protein-ligand binding constants using electrospray ionization mass spectrometry: a systematic binding affinity study of a series of hydrophobically modified trypsin inhibitors
Q30278887Structure of BbKI, a disulfide-free plasma kallikrein inhibitor
Q30605285Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity.
Q48031360Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
Q37364377Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
Q33642484Trypsin-ligand binding free energy calculation with AMOEBA.
Q34975702Virtual screening using molecular simulations

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