MOTIVATION: Advances in the field of cheminformatics have been hindered by a lack of freely available tools. We have created Chembench, a publicly available cheminformatics portal for analyzing experimental chemical structure-activity data. Chembench provides a broad range of tools for data visualization and embeds a rigorous workflow for creating and validating predictive Quantitative Structure-Activity Relationship models and using them for virtual screening of chemical libraries to prioritize the compound selection for drug discovery and/or chemical safety assessment. AVAILABILITY: Freely accessible at: http://chembench.mml.unc.edu CONTACT: [email protected]

UNLABELLED: We built a novel web-based platform for performing discrete molecular dynamics simulations of proteins. In silico protein folding involves searching for minimal frustration in the vast conformational landscape. Conventional approaches for simulating protein folding insufficiently address the problem of simulations in relevant time and length scales necessary for a mechanistic understanding of underlying biomolecular phenomena. Discrete molecular dynamics (DMD) offers an opportunity to bridge the size and timescale gaps and uncover the structural and biological properties of experimentally undetectable protein dynamics. The iFold server supports large-scale simulations of protein folding, thermal denaturation, thermodynamic scan, simulated annealing and p(fold) analysis using DMD and coarse-grained protein model with structure-based Gō-interactions between amino acids. AVAILABILITY: http://ifold.dokhlab.org

The multiprotocol transport networking (MPTN) architecture proposed in this paper is a general solution to providing interconnectivity for applications. The MPTN architecture provides a protocol-independent system interface that includes most functions provided by existing transport protocols. As a result, the MPTN architecture decouples higher-layer protocols, application programming interfaces, and applications from protocols at the transport layer and below. Using the MPTN architecture, current and new applications can function unmodified over any transport supported under the MPTN interface. In addition, MPTN transport-layer gateways provide an end-to-end communication facility across a number of networks running different protocols. Therefore, a collection of networks running different protocols can serve as a single logical network.>

This paper discusses SNA/LEN, a possible extension of Systems Network Architecture intended to allow peer, dynamic, and easy to use networking functions for a variety of node sizes down to and including the new generation of personal computers. After reviewing the special requirements posed by small systems and the need for including them as equal partners in networks, the LEN architecture is described. This is done by following a sequence of steps that begin when a logical resource at some node that may not yet be part of the connectivity of an existing network requests a session with a remote logical resource of unknown location. After connectivity with the preexisiting network is established, directory services locates the remote object, route selection services determines the preferred path, a session is activated, and deadlock-free flow control assures a useful flow of data. Preliminary quantitative results from an LEN prototype are presented.

IBM's Systems Network Architecture (SNA) is formally defined by a meta-implementation program written in the Format and Protocol Language (FAPL). This paper describes the structure of the SNA meta-implementation and the development of FAPL. The most interesting aspect of the meta-implementation is that the architecture specification of SNA is itself machine executable. This property leads to a number of applications in software technology, such as automated protocol validation and direct Implementation from the formal specification.

A space-efficient strategy for storing attributes during evaluation of an attribute grammar is presented.Attributes are classified as either one-pass or multipass.One-pass attributes are stored on a pushdown stack, and their storage is freed when no longer needed.Examination of extant grammars shows that a vast majority of attributes are indeed one-pass, and therefore the scheme presented can greatly reduce the storage requirements of an attribute grammar evaluator.Several approaches to storage management for multipass attributes are also presented.Data for several grammars are collected and used to show the effectiveness of the proposed storage management scheme.