Visible Volume: a Robust Measure for Protein Structure Characterization

We propose a new characterization of protein structure based on the natural tetrahedral geometry of the β carbon and a new geometric measure of structural similarity, called visible volume. In our model, the side-chains are replaced by an ideal tetrahedron, the orientation of which is fixed with respect to the backbone and corresponds to the preferred rotamer directions. Visible volume is a measure of the non-occluded empty space surrounding each residue position after the side-chains have been removed. It is a robust, parameter-free, locally-computed quantity that accounts for many of the spatial constraints that are of relevance to the corresponding position in the native structure. When computing visible volume, we ignore the nature of both the residue observed at each site and the ones surrounding it. We focus instead on the space that, together, these residues could occupy. By doing so, we are able to quantify a new kind of invariance beyond the apparent variations in protein families, namely, the conservation of the physical space available at structurally equivalent positions for side-chain packing. Corresponding positions in native structures are likely to be of interest in protein structure prediction, protein design, and homology modeling. Visible volume is related to the degree of exposure of a residue position and to the actual rotamers in native proteins. In this article, we discuss the properties of this new measure, namely, its robustness with respect to both crystallographic uncertainties and naturally occurring variations in atomic coordinates, and the remarkable fact that it is essentially independent of the choice of the parameters used in calculating it. We also show how visible volume can be used to align protein structures, to identify structurally equivalent positions that are conserved in a family of proteins, and to single out positions in a protein that are likely to be of biological interest. These properties qualify visible volume as a powerful tool in a variety of applications, from the detailed analysis of protein structure to homology modeling, protein structural alignment, and the definition of better scoring functions for threading purposes.

Load Profiling for Efficient Route Selection in Multi-Class Networks

High-speed networks, such as ATM networks, are expected to support diverse Quality of Service (QoS) constraints, including real-time QoS guarantees. Real-time QoS is required by many applications such as those that involve voice and video communication. To support such services, routing algorithms that allow applications to reserve the needed bandwidth over a Virtual Circuit (VC) have been proposed. Commonly, these bandwidth-reservation algorithms assign VCs to routes using the least-loaded concept, and thus result in balancing the load over the set of all candidate routes. In this paper, we show that for such reservation-based protocols|which allow for the exclusive use of a preset fraction of a resource's bandwidth for an extended period of time-load balancing is not desirable as it results in resource fragmentation, which adversely affects the likelihood of accepting new reservations. In particular, we show that load-balancing VC routing algorithms are not appropriate when the main objective of the routing protocol is to increase the probability of finding routes that satisfy incoming VC requests, as opposed to equalizing the bandwidth utilization along the various routes. We present an on-line VC routing scheme that is based on the concept of "load profiling", which allows a distribution of "available" bandwidth across a set of candidate routes to match the characteristics of incoming VC QoS requests. We show the effectiveness of our load-profiling approach when compared to traditional load-balancing and load-packing VC routing schemes.

Evaluation of a Load Profiling Approach to Routing Guaranteed Bandwidth Flows

To support the diverse Quality of Service (QoS) requirements of real-time (e.g. audio/video) applications in integrated services networks, several routing algorithms that allow for the reservation of the needed bandwidth over a Virtual Circuit (VC) established on one of several candidate routes have been proposed. Traditionally, such routing is done using the least-loaded concept, and thus results in balancing the load across the set of candidate routes. In a recent study, we have established the inadequacy of this load balancing practice and proposed the use of load profiling as an alternative. Load profiling techniques allow the distribution of "available" bandwidth across a set of candidate routes to match the characteristics of incoming VC QoS requests. In this paper we thoroughly characterize the performance of VC routing using load profiling and contrast it to routing using load balancing and load packing. We do so both analytically and via extensive simulations of multi-class traffic routing in Virtual Path (VP) based networks. Our findings confirm that for routing guaranteed bandwidth flows in VP networks, load balancing is not desirable as it results in VP bandwidth fragmentation, which adversely affects the likelihood of accepting new VC requests. This fragmentation is more pronounced when the granularity of VC requests is large. Typically, this occurs when a common VC is established to carry the aggregate traffic flow of many high-bandwidth real-time sources. For VP-based networks, our simulation results show that our load-profiling VC routing scheme performs better or as well as the traditional load-balancing VC routing in terms of revenue under both skewed and uniform workloads. Furthermore, load-profiling routing improves routing fairness by proactively increasing the chances of admitting high-bandwidth connections.