NOEnet–Use of NOE networks for NMR resonance assignment of proteins with known 3D structure

Motivation: A prerequisite for any protein study by NMR is the assignment of the resonances from the 15N−1H HSQC spectrum to their corresponding atoms of the protein backbone. Usually, this assignment is obtained by analyzing triple resonance NMR experiments. An alternative assignment strategy exploits the information given by an already available 3D structure of the same or a homologous protein. Up to now, the algorithms that have been developed around the structure-based assignment strategy have the important drawbacks that they cannot guarantee a high assignment accuracy near to 100%

On the Power of Threshold-Based Algorithms for Detecting Cycles in the CONGEST Model

It is known that, for every $k\geq 2$, $C_{2k}$-freeness can be decided by a generic Monte-Carlo algorithm running in $n^{1-1/\Theta(k^2)}$ rounds in the CONGEST model. For $2\leq k\leq 5$, faster Monte-Carlo algorithms do exist, running in $O(n^{1-1/k})$ rounds, based on upper bounding the number of messages to be forwarded, and aborting search sub-routines for which this number exceeds certain thresholds. We investigate the possible extension of these threshold-based algorithms, for the detection of larger cycles. We first show that, for every $k\geq 6$, there exists an infinite family of graphs containing a $2k$-cycle for which any threshold-based algorithm fails to detect that cycle. Hence, in particular, neither $C_{12}$-freeness nor $C_{14}$-freeness can be decided by threshold-based algorithms. Nevertheless, we show that $\{C_{12},C_{14}\}$-freeness can still be decided by a threshold-based algorithm, running in $O(n^{1-1/7})= O(n^{0.857\dots})$ rounds, which is faster than using the generic algorithm, which would run in $O(n^{1-1/22})\simeq O(n^{0.954\dots})$ rounds. Moreover, we exhibit an infinite collection of families of cycles such that threshold-based algorithms can decide $\mathcal{F}$-freeness for every $\mathcal{F}$ in this collection.Comment: to be published in SIROCCO 202

The Communication Complexity of Set Intersection and Multiple Equality Testing

In this paper we explore fundamental problems in randomized communication complexity such as computing Set Intersection on sets of size $k$ and Equality Testing between vectors of length $k$. Sa\u{g}lam and Tardos and Brody et al. showed that for these types of problems, one can achieve optimal communication volume of $O(k)$ bits, with a randomized protocol that takes $O(\log^* k)$ rounds. Aside from rounds and communication volume, there is a \emph{third} parameter of interest, namely the \emph{error probability} $p_{\mathrm{err}}$. It is straightforward to show that protocols for Set Intersection or Equality Testing need to send $\Omega(k + \log p_{\mathrm{err}}^{-1})$ bits. Is it possible to simultaneously achieve optimality in all three parameters, namely $O(k + \log p_{\mathrm{err}}^{-1})$ communication and $O(\log^* k)$ rounds? In this paper we prove that there is no universally optimal algorithm, and complement the existing round-communication tradeoffs with a new tradeoff between rounds, communication, and probability of error. In particular: 1. Any protocol for solving Multiple Equality Testing in $r$ rounds with failure probability $2^{-E}$ has communication volume $\Omega(Ek^{1/r})$. 2. There exists a protocol for solving Multiple Equality Testing in $r + \log^*(k/E)$ rounds with $O(k + rEk^{1/r})$ communication, thereby essentially matching our lower bound and that of Sa\u{g}lam and Tardos. Our original motivation for considering $p_{\mathrm{err}}$ as an independent parameter came from the problem of enumerating triangles in distributed ($\textsf{CONGEST}$) networks having maximum degree $\Delta$. We prove that this problem can be solved in $O(\Delta/\log n + \log\log \Delta)$ time with high probability $1-1/\operatorname{poly}(n)$.Comment: 44 page

Robust structure-based resonance assignment for functional protein studies by NMR

High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment approach using mainly HN–HN NOEs networks, as well as 1H–15N residual dipolar couplings and chemical shifts. The NOEnet complete search algorithm is robust against assignment errors, even for sparse input data. Instead of a unique and partly erroneous assignment solution, an optimal assignment ensemble with an accuracy equal or near to 100% is given by NOEnet. We show that even low precision assignment ensembles give enough information for functional studies, like modeling of protein-complexes. Finally, the combination of NOEnet with a low number of ambiguous J-coupling sequential connectivities yields a high precision assignment ensemble. NOEnet will be available under: http://www.icsn.cnrs-gif.fr/download/nmr