Supervised consensus scoring for docking and virtual screening

Docking programs are widely used to discover novel ligands efficiently and can predict protein-ligand complex structures with reasonable accuracy and speed. However, there is an emerging demand for better performance from the scoring methods. Consensus scoring (CS) methods improve the performance by compensating for the deficiencies of each scoring function. However, conventional CS and existing scoring functions have the same problems, such as a lack of protein flexibility, inadequate treatment of salvation, and the simplistic nature of the energy function used. Although there are many problems in current scoring functions, we focus our attention on the incorporation of unbound ligand conformations. To address this problem, we propose supervised consensus scoring (SCS), which takes into account protein-ligand binding process using unbound ligand conformations with supervised learning. An evaluation of docking accuracy for 100 diverse protein-ligand complexes shows that SCS outperforms both CS and 11 scoring functions (PLP, F-Score, LigScore, DrugScore, LUDI, X-Score, AutoDock, PMF, G-Score, ChemScore, and D-score). The success rates of SCS range from 89% to 91% in the range of rmsd < 2 A, while those of CS range from 80% to 85%, and those of the scoring functions range from 26% to 76%. Moreover, we also introduce a method for judging whether a compound is active or inactive with the appropriate criterion for virtual screening. SCS performs quite well in docking accuracy and is presumably useful for screening large-scale compound databases before predicting binding affinity.     

A Characterization of Right Coideals of Quotient Type and its Application to Classification of Poisson Boundaries

Let be a co-amenable compact quantum group. We show that a right coideal of is of quotient type if and only if it is the range of a conditional expectation preserving the Haar state and is globally invariant under the left action of the dual discrete quantum group. We apply this result to the theory of Poisson boundaries introduced by Izumi for discrete quantum groups and generalize a work of Izumi-Neshveyev-Tuset on SU _q (N) for co-amenable compact quantum groups with the commutative fusion rules. More precisely, we prove that the Poisson integral is an isomorphism between the Poisson boundary and the right coideal of quotient type by a maximal quantum subgroup of Kac type. In particular, the Poisson boundary and the quantum flag manifold are isomorphic for any q-deformed classical compact Lie group.     

Modulation of a Molecular π‐Electron System in a Purely Organic Conductor that Shows Hydrogen‐Bond‐Dynamics‐Based Switching of Conductivity and Magnetism

New important aspects of the hydrogen‐bond (H‐bond)‐dynamics‐based switching of electrical conductivity and magnetism in an H‐bonded, purely organic conductor crystal have been discovered by modulating its tetrathiafulvalene (TTF)‐based molecular π‐electron system by means of partial sulfur/selenium substitution. The prepared selenium analogue also showed a similar type of phase transition, induced by H‐bonded deuterium transfer followed by electron transfer between the H‐bonded TTF skeletons, and the resulting switching of the physical properties; however, subtle but critical differences due to sulfur/selenium substitution were detected in the electronic structure, phase transition nature, and switching function. A molecular‐level discussion based on the crystal structures shows that this chemical modification of the TTF skeleton influences not only its own π‐electronic structure and π–π interactions within the conducting layer, but also the H‐bond dynamics between the TTF π skeletons in the neighboring layers, which enables modulation of the interplay between the H‐bond and π electrons to cause such differences.     

A carbon nanotube structured biomimetic catalyst for polysaccharide degradation

A unique artificial catalyst that mimics the structure of active sites in real enzymes using functionalized carbon nanotubes is presented. This concept will allow for the potential construction of a library of biomimetic catalysts for enzyme active centers, for which the structure-catalysis relationships are well defined.     

Iron-catalyzed δ-selective conjugate addition of methyl and cyclopropyl Grignard reagents to α,β,γ,δ-unsaturated esters and amides

Iron-catalyzed δ-selective conjugate addition of methyl and cyclopropyl Grignard reagents to α,β,γ,δ-unsaturated esters and amides took place in good yields to give products exclusively with cis-β,γ-olefinic bond.     

Atomic and electronic structure of microclusters

The atomic and electronic structure of alkali metal, noble metal and Si_N (N=6,10) clusters examined theoretically are reviewed. On metal clusters, validity of the spherical jellium model is discussed by examining stabilization by multiplets formation and crystalline fields. In connection with the fragmentation of metal clusters, the shell correction of a largely deformed metal clusters is discussed by referring to Strutinsky's theory of nuclear fission. On the Si₆ and Si₁₀ clusters a large reconstruction theoretically found is discussed in terms of the interaction among dangling bonds. Finally, recent work on dynamical properties of clusters are briefly reviewed.     

Synthesis of indoles via amidoselenation

The reaction of 2-styrylacetanilides (2) with N-phenylselenosuccinimide affords 1-N-acetyl-2-phenyl-3-phenylselenoindoles (3) and 1-N-acetyl-2-phenylindoles (4) . The reaction of 2-vinylacetanilides (5) with phenylselenenyl bromide proceeds to form indoles via an intramolecular amidoselenation.     

Shell effects on symmetric fragmentations of alkali-metal clusters

Symmetric fragmentation of multiply charged alkali-metal clusters consisting of several tens of atoms is studied. The energy variation during the fragmentation process is calculated using the theory ofshell corrections, in which total energy is written as a sum of the liquid-droplet and shell correction terms. It is found that the variation of the shell correction term is much larger than that of the liquid-droplet one if the parent cluster is metastable. Fragmentation into nearly-magic cluster is most favored regardless of parent size since the barrier height for fragmentation is mainly determined by the shell configuration of fragments rather than that of the parent.