the default is to apply built-in pKa model to determine predominant protonation state. To keep protonation as in input sdf, you can turn this off with _dockBatch -u option (or change it in
In recent years, conventional chemistry techniques have faced significant challenges due to their inherent limitations, struggling to cope with the increas
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Different strategies have been employed to determine the most likely binding configurations out of these multiple outcomes. Often, these approaches are based on additional refined simulations or statistical analysis of the large number of binding conformations. [56–58]. We employed a different approach...
Central to this challenging area of structural biology was the deployment of NMR as a key method to determine the compositions and structures of the carbohydrate components of glycoproteins. The PDB has welcomed NMR structures for many years, and glycoproteins represented an example where synergistic ...
The first Nuclear Magnetic Resonance (NMR) beams were detected in the 1930s by a team of researchers from Columbia University in New York City. Click to read more...
Biochemistry studies the chemical processes within and related to living organisms. It is a laboratory-based science that combines biology and chemistry, often focusing on the molecular level of life. Structure and function of enzymes in metabolic pathways ...
How to determine bond order from molecular electron configuration Determine which molecules are chiral Determine the Lewis structure for CH_2 Br_2, with polarity and noting if it is symmetrical. What is orbital resonance? How to figure out polarity of a molecule ...
Comparing to a generic two-state model, our models can distinguish class I from class II MHCs and correlate their structural parameters with the TCR/pMHC’s potency to trigger T cell activation. The models are tested by mutagenesis using an MHC and a TCR mutated to alter conformation changes....
Collectively, these data provide mechanistic explanations for how intramolecular and intermolecular interactions determine the site-specific functions of FAK. In the following we briefly outline how this framework may explain FAK's different actions in different subcellular environments. Sections 9.1 FAK in...