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A study involved the measurement of the kinematic values of attractant binding of the ligand region of chemotaxis aspartate receptor. The structural regions involved in attractant-induced conformational change were located. Each subunit of the homodimer revealed six parafluorophenylalanine (4-F-Phe) positions. The dissociation rate constant (k-off approximately equal to 10 cubed per second) was calculated from the association rate constant (K-on approximately equal to 10 to the 9th power meter per second) of the bond between the isolated periplasmic domain and the aspartate.

An analysis of structural, chemical and cooperative properties of Escherichia coli and Salmonella typhimurium aspartate receptors reveals that both have specific negatively cooperative binding configurations. Amino acid sequences for aspartate receptors have 79% identity but the E. coli receptor exhibits single site binding. Consequently, the E. coli receptor binds with 'half-of-the sites' cooperativity, where the E. coli receptor's second ligand does not bind.

We have studied the subtleties of fragment docking and binding using data generated in a Pim-1 kinase inhibitor program. Crystallographic and docking data analyses have been undertaken using inhibitor complexes derived from an in-house surface plasmon resonance (SPR) fragment screen, a virtual needle screen, and a de novo designed fragment inhibitor hybrid. These investigations highlight that fragments that do not fill their binding pocket can exhibit promiscuous hydrophobic interactions due to the lack of steric constraints imposed on them by the boundaries of said pocket. As a result, docking modes that disagree with an observed crystal structure but maintain key crystallographically observed hydrogen bonds still have potential value in ligand design and optimization. This observation runs counter to the lore in fragment-based drug design that all fragment elaboration must be based on the parent crystal structure alone.