1,144 research outputs found
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
machines jointly perform computations on graphs with nodes (typically, ). The input graph is assumed to be initially randomly partitioned among
the 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 degree connected network, in which
every search succeeds in hops w.h.p., using messages,
where 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 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
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