Multilevel Parallelization of AutoDock 4.2

<p>Abstract</p> <p>Background</p> <p>Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4).</p> <p>Results</p> <p>Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O) traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers.</p> <p>Conclusions</p> <p>Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI) and node-level (OpenMP) parallelization to best fit both workloads and computational resources.</p

Before It Gets Started: Regulating Translation at the 5′ UTR

Translation regulation plays important roles in both normal physiological conditions and diseases states. This regulation requires cis-regulatory elements located mostly in 5′ and 3′ UTRs and trans-regulatory factors (e.g., RNA binding proteins (RBPs)) which recognize specific RNA features and interact with the translation machinery to modulate its activity. In this paper, we discuss important aspects of 5′ UTR-mediated regulation by providing an overview of the characteristics and the function of the main elements present in this region, like uORF (upstream open reading frame), secondary structures, and RBPs binding motifs and different mechanisms of translation regulation and the impact they have on gene expression and human health when deregulated

Identification of diverse cohesin-independent SA interactors that inform SA-specific functions

Cohesin complexes regulate genome organisation throughout the cell cycle. The molecular mechanisms by which cohesin governs this regulation are still not fully understood. SA1 and SA2 (SA) proteins are critical for cohesin function and are currently considered as core members of the complex due to their ubiquitous interaction with the ring protein members. This thesis investigates the role of the SA proteins in mediating interaction with CTCF. This work determines that following acute depletion of RAD21, SA proteins remain on chromatin and in complex with CTCF. The SA-CTCF interaction is dependent on the presence of nucleic acids and is localised at canonical cohesin binding sites in the genome. Mass spectrometry analysis further determines that cohesin-independent SA1, at least, does not just interact with CTCF, but also a range of additional proteins. The interactome of SA1 in the presence and absence of cohesin is identified. The SA1 interactome includes a wide variety of proteins spanning chromosome organisation, transcription, RNA processing, ribosome biogenesis, and translation. This thesis further reveals that cohesin-independent SA1 is enriched to proteins involved in RNA processing and ribosome biogenesis. R-loop proteins are highly enriched in the SA1 interactome and have previously been identified at sites encompassing all of these processes. Interaction of SA with R-loop structures and RNA itself is confirmed. A functional role for cohesin-independent SA is revealed in the association of cohesin with chromatin in the presence or absence of the NIPBL/MAU2 loader complex. While cohesin is found to load onto chromatin most efficiently in the presence of both SA and NIPBL/MAU2, this work reveals that SA alone can induce cohesin loading in a manner that is specifically linked to the abundance of R-loop structures present in the cell

Evaluation and Implementation of a Discovery Tool

The buzz in campus libraries is Discovery Tools -- how they work and how our patrons use them. But first, a library needs to evaluate and implement the discovery product. Experiences with Pittsburg State University\u27s implementation of Serials Solutions\u27 Summon product are presented, along with a select bibliography of early implementer literature, as a guide to successful implementation for the small- to medium-sized library

Global Diffusion of the Internet XV: Web 2.0 Technologies, Principles, and Applications: A Conceptual Framework from Technology Push and Demand Pull Perspective

Web 2.0, the current Internet evolution, can be described by several key features of an expanded Web that is more interactive; allows easy social interactions through participation and collaboration from a variety of human sectors; responds more immediately to users\u27 queries and needs; is easier to search; and provides a faster, smoother, realistic and engaging user search capability, often with automatic updates to users. The purpose of this study is three-fold. First, the primary goal is to propose a conceptual Web 2.0 framework that provides better understanding of the Web 2.0 concept by classifying current key components in a holistic manner. Second, using several selective key components from the conceptual framework, this study conducts case analyses of Web 2.0 applications to discuss how they have adopted the selective key features (i.e., participation, collaboration, rich user experience, social networking, semantics, and interactivity responsiveness) of the conceptual Web 2.0 framework. Finally, the study provides insightful discussion of some challenges and opportunities provided by Web 2.0 to education, business, and social life