Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

Summary AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.The AutoDock 2.4 suite is written in ANSI C, and is supplied with Makefiles for the following platforms: Convex, DEC Alpha OSF/1, Hewlett-Packard Precision Architecture, Silicon Graphics, and Sun. The AutoDock suite of programs is freely available to the noncommercial scientific community and to educational establishments. Further information, including additional figures and MPEG animations showing all docked conformations for each test system, can be found at the following URL: http://www.scripps.edu/pub/olson-web/doc/autodock.     

Rate enhancement for nitroxide stable free radical polymerization of n‐butyl acrylate by dodecylbenzenesulfonic acid

Dodecylbenzenesulfonic acid, DDBSA, was chosen as a new rate‐accelerating additive for 2,2,6,6,‐teramethyl‐1‐piperidinyloxy (TEMPO)‐mediated stable free radical polymerization of n‐butyl acrylate (n‐BA) monomers with 2,2′‐azobisisobutyronitrile (AIBN). It was found that the number‐average molecular weight of polymers could reach about ten thousand with a narrow polydispersity index (PDI) of 1.4 in a few minutes, which was faster than other systems reported previously. But, at higher conversion, the molecular weight distribution of polymers became broad, and a bimodal distribution occurred. The macro‐initiators isolated from the former polymers with narrow PDI could be extended by polymerization with monomers by the addition of DDBSA. Furthermore, a proposed kinetic model demonstrated that the decay of the concentration of DDBSA would reduce the living polymer concentration and retard the growth of the polymers, which could be further propagated by the supplement of DDBSA. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 42–49, 2005     

Perturbations of Pseudodifferential Operators with Negative Definite Symbol

Pseudodifferential operators with negative definite symbols appear as generators of jump-type Markov processes. The purpose of this paper is to treat the large jumps of the process by a perturbation approach for the generator. This is of particular interest since in this way the generators are made accessible to a symbolic calculus of pseudodifferential operators. The main auxiliary result consists of a characterization of tightness of the jump measures in terms of the symbol.     

Phytoquinoids and Secoprezizaane‐Type Sesquiterpenes from Illicium arborescens

A phytochemical investigation of the MeOH extract of Illicium arborescens yielded the two new phytoquinoid epimers, 2,3‐didehydro‐5‐O‐methyl‐11‐epiillifunone E ( 1 ) and 2,3‐didehydro‐5‐O‐methylillifunone E ( 2 ), as well as five new sesquiterpene lactones (8,9‐secoprezizaane‐type sesquiterpenes). Two of them, i.e., 3 and 4 , were minwanensin‐type sesquiterpenes, the other two, i.e., 5 and 6 , had the anisatin‐type (or floridanolide type) skeleton, and the fifth, i.e., 7 , was a dunnianin‐type sesquiterpene. Their structures were established by analyses of 1D‐ and 2D‐NMR, HR‐MS, and chemical evidence. The in vitro cytotoxic activity of compounds 1 – 7 was tested against four human tumor cell lines, including HeLa (cervical epitheloid), WiDr (colon), Daoy (medulloblastoma), and Hep2 (liver carcinoma) human‐tumor cells.     

Costly punishment and cooperation in the evolutionary snowdrift game

The role of punishments in promoting cooperation is an important issue. We incorporate costly punishments into the snowdrift game (SG) by introducing a third punishing (P) character, and study the effects. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α so as to punish a non-cooperative (D) opponent by β. Depending on the initial fractions of the characters, α, β, and the cost-to-benefit ratio r in the SG, the three-character system evolves into a steady state consisting either only of C and P characters or only of C and D characters, in a well-mixed population. The former situation represents an enhancement in cooperation relative to the SG, while the latter is similar to the SG. The dynamics in approaching these different steady states are found to be different. Analytically, the key features in the dynamics and the steady states observed in simulations are captured by a set of differential equations. The sensitivity to the initial distribution of characters is studied by depicting the flow in a phase portrait and analyzing the nature of fixed points. The analysis also shows the role of P-character agents in preventing a system from invasion by D-character agents. Starting from a population consisting only of C and P agents, a D-character agent intended to invade the system cannot survive when the initial fraction of P agents is greater than r/β. Our model, defined intentionally as a simulation algorithm, can be readily generalized to incorporate many interesting effects, such as those in a networked population.     

A channel estimation algorithm for MIMO-SCFDE

This letter proposes a novel method for channel estimation in a single-carrier multiple input-multiple output (MIMO) system with frequency-domain equalization/detection. To this end, we construct novel short MIMO training sequences that have constant envelope in the time domain to preclude the peak-to-average power ratio problem encountered in many systems that utilize the frequency domain for data recovery. Simultaneously, the spectrum in the frequency domain is flat except for a grid of s for predefined frequency tones. Armed with these sequences, we provide an algorithm that is optimal in the least squares (LS) sense at a potentially low computational cost. Results show that the algorithm performs identically to other proposed LS techniques. Furthermore, the algorithm is extremely bandwidth efficient in that the total training overhead required to obtain full CSI is just one block.     

Organocatalyzed Asymmetric Conjugate Addition of Heteroaryl and Aryl Trifluoroborates: a Synthetic Strategy for Discoipyrrole D

Bis‐heteroaryl or bis‐aryl stereocenters were formed by an organocatalytic enantioselective conjugate addition using the respective trifluoroborate salts as nucleophiles. Control studies suggested that fluoride dissociation is necessary in the anhydrous conditions. This strategy is applicable to the synthesis of discoipyrrole D, an inhibitor of BR5 fibroblast migration.