Target selection is a critical step in the majority of modern drug discovery programs. The viability of a drug target depends on two components: biological relevance and chemical tractability. The concept of druggability was introduced to describe the second component, and it is defined as the ability of a target to bind a drug-like molecule with a therapeutically useful level of affinity. To i...

This paper argues that a commitment to ‘shallow pockets’, namely by limiting the size of funds raised initially, may improve an investor’s ability to deal with entrepreneurial agency problems. Shallow pockets allow the investor to create competition for continuation finance between her portfolio entrepreneurs. Although this increases the investor’s ex post bargaining power vis-à-vis entrepreneu...

We observe apparent hole pockets in the Fermi surfaces of single-layer Bi-based cuprate superconductors from angle-resolved photoemission. From detailed low-energy electron diffraction measurements and an analysis of the angle-resolved photoemission polarization dependence, we show that these pockets are not intrinsic but arise from multiple overlapping superstructure replicas of the main and s...

Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as "binding-pockets," which enhance the stability. Us...

We developed a new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites. We performed a large scale classification of the identified envelopes according to their shape and physicochemical properties. The predicting algorithm, called PocketFinder, uses a transformation of the Lennard-Jones potential calculated from a three-dimensio...

This research was carried out to follow-up the microbial growth-down rates of the inflammatory periodontal pockets using radiotherapy, Taif Region, KSA. The patients (Pts.) under study were (No.=25pts.),they had chronic pockets periodontitis, they were divided into 20Pts. as study group (SG) and 5Pts. as control group (CG). SG had received radiotherapy (RT) and CG had received irrigation with n...

Peptide binding to class II MHC protein is commonly viewed as a combination of discrete anchor residue preferences for pockets 1, 4, 6/7, and 9. However, previous studies have suggested cooperative effects during the peptide binding process. Investigation of the DRB1*0901 binding motif demonstrated a clear interaction between peptide binding pockets 6 and 9. In agreement with prior studies, poc...

Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings. Structural studies have shown that in many cases, the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its protein-bound conformations. This plasticity of the protein surface presents a maj...