RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps

Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies in the fitted component. Results: Here we present the RIBFIND server, a tool for identifying rigid bodies in protein structures. The server identifies rigid bodies in proteins by calculating spatial proximity between their secondary structural elements. Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk

On the Distributed Complexity of Large-Scale Graph Computations

Motivated by the increasing need to understand the distributed algorithmic foundations of large-scale graph computations, we study some fundamental graph problems in a message-passing model for distributed computing where $k \geq 2$ machines jointly perform computations on graphs with $n$ nodes (typically, $n \gg k$). The input graph is assumed to be initially randomly partitioned among the $k$ machines, a common implementation in many real-world systems. Communication is point-to-point, and the goal is to minimize the number of communication {\em rounds} of the computation. Our main contribution is the {\em General Lower Bound Theorem}, a theorem that can be used to show non-trivial lower bounds on the round complexity of distributed large-scale data computations. The General Lower Bound Theorem is established via an information-theoretic approach that relates the round complexity to the minimal amount of information required by machines to solve the problem. Our approach is generic and this theorem can be used in a "cookbook" fashion to show distributed lower bounds in the context of several problems, including non-graph problems. We present two applications by showing (almost) tight lower bounds for the round complexity of two fundamental graph problems, namely {\em PageRank computation} and {\em triangle enumeration}. Our approach, as demonstrated in the case of PageRank, can yield tight lower bounds for problems (including, and especially, under a stochastic partition of the input) where communication complexity techniques are not obvious. Our approach, as demonstrated in the case of triangle enumeration, can yield stronger round lower bounds as well as message-round tradeoffs compared to approaches that use communication complexity techniques

Stochastic Analysis of a Churn-Tolerant Structured Peer-to-Peer Scheme

We present and analyze a simple and general scheme to build a churn (fault)-tolerant structured Peer-to-Peer (P2P) network. Our scheme shows how to "convert" a static network into a dynamic distributed hash table(DHT)-based P2P network such that all the good properties of the static network are guaranteed with high probability (w.h.p). Applying our scheme to a cube-connected cycles network, for example, yields a $O(\log N)$ degree connected network, in which every search succeeds in $O(\log N)$ hops w.h.p., using $O(\log N)$ messages, where $N$ is the expected stable network size. Our scheme has an constant storage overhead (the number of nodes responsible for servicing a data item) and an $O(\log N)$ overhead (messages and time) per insertion and essentially no overhead for deletions. All these bounds are essentially optimal. While DHT schemes with similar guarantees are already known in the literature, this work is new in the following aspects: (1) It presents a rigorous mathematical analysis of the scheme under a general stochastic model of churn and shows the above guarantees; (2) The theoretical analysis is complemented by a simulation-based analysis that validates the asymptotic bounds even in moderately sized networks and also studies performance under changing stable network size; (3) The presented scheme seems especially suitable for maintaining dynamic structures under churn efficiently. In particular, we show that a spanning tree of low diameter can be efficiently maintained in constant time and logarithmic number of messages per insertion or deletion w.h.p. Keywords: P2P Network, DHT Scheme, Churn, Dynamic Spanning Tree, Stochastic Analysis