This article presents a study of the literature of chemoinformatics, updating and building upon an analogous bibliometric investigation that was published in 2008. Data on outputs in the field, and ...citations to those outputs, were obtained by means of topic searches of the
. The searches demonstrate that chemoinformatics is by now a well-defined sub-discipline of chemistry, and one that forms an essential part of the chemical educational curriculum. There are three core journals for the subject: The
, the
, and
, and, having established itself, chemoinformatics is now starting to export knowledge to disciplines outside of chemistry.
This chapter reviews the use of molecular fingerprints for chemical similarity searching. The fingerprints encode the presence of 2D substructural fragments in a molecule, and the similarity between ...a pair of molecules is a function of the number of fragments that they have in common. Although this provides a very simple way of estimating the degree of structural similarity between two molecules, it has been found to provide an effective and an efficient tool for searching large chemical databases. The review describes the historical development of similarity searching since it was first described in the mid-1980s, reviews the many different coefficients, representations, and weightings that can be combined to form a similarity measure, describes quantitative measures of the effectiveness of similarity searching, and concludes by looking at current developments based on the use of data fusion and machine learning techniques.
This paper summarizes recent work at the University of Sheffield on virtual screening methods that use 2D fingerprint measures of structural similarity. A detailed comparison of a large number of ...similarity coefficients demonstrates that the well-known Tanimoto coefficient remains the method of choice for the computation of fingerprint-based similarity, despite possessing some inherent biases related to the sizes of the molecules that are being sought. Group fusion involves combining the results of similarity searches based on multiple reference structures and a single similarity measure. We demonstrate the effectiveness of this approach to screening, and also describe an approximate form of group fusion, turbo similarity searching, that can be used when just a single reference structure is available.
This paper discusses the use of binary-encoded fragment substructures to scan databases to find molecules that are structurally similar to a bioactive query compound.
This commentary provides an overview of the publications in, and the citations to, the first twelve volumes of the Journal of Cheminformatics, covering the period 2009-2020. The analysis is based on ...the 622 articles that have appeared in the journal during that time and that have been indexed in the Clarivate Web of Science Core Collection database. It is clear that the journal has established itself as one of the most important publications in the field of cheminformatics: it attracts citations not only from other journals in its specialist field but also from biological and chemical journals more widely, and moreover from journals that are far removed in focus from it but that are still able to benefit from the articles that it publishes.
To prevent the outbreak of the Coronavirus disease (COVID-19), many countries around the world went into lockdown and imposed unprecedented containment measures. These restrictions progressively ...produced changes to social behavior and global mobility patterns, evidently disrupting social and economic activities. Here, using maritime traffic data collected via a global network of Automatic Identification System (AIS) receivers, we analyze the effects that the COVID-19 pandemic and containment measures had on the shipping industry, which accounts alone for more than 80% of the world trade. We rely on multiple data-driven maritime mobility indexes to quantitatively assess ship mobility in a given unit of time. The mobility analysis here presented has a worldwide extent and is based on the computation of: Cumulative Navigated Miles (CNM) of all ships reporting their position and navigational status via AIS, number of active and idle ships, and fleet average speed. To highlight significant changes in shipping routes and operational patterns, we also compute and compare global and local vessel density maps. We compare 2020 mobility levels to those of previous years assuming that an unchanged growth rate would have been achieved, if not for COVID-19. Following the outbreak, we find an unprecedented drop in maritime mobility, across all categories of commercial shipping. With few exceptions, a generally reduced activity is observable from March to June 2020, when the most severe restrictions were in force. We quantify a variation of mobility between -5.62 and -13.77% for container ships, between +2.28 and -3.32% for dry bulk, between -0.22 and -9.27% for wet bulk, and between -19.57 and -42.77% for passenger traffic. The presented study is unprecedented for the uniqueness and completeness of the employed AIS dataset, which comprises a trillion AIS messages broadcast worldwide by 50,000 ships, a figure that closely parallels the documented size of the world merchant fleet.
We deal with the classical problem of testing two simple statistical hypotheses but, as a new element, it is assumed that the data vector is observed after an unknown permutation of its entries. What ...is the fundamental limit for the detection performance in this case? How much information for detection is contained in the entry values and how much in their positions? In the first part of this paper, we answer these questions. In the second part, we focus on practical algorithms. A low-complexity detector solves the detection problem without attempting to estimate the permutation. A modified version of the auction algorithm is then considered, and two greedy algorithms with affordable worst case complexity are presented. The detection operational characteristics of these detectors are investigated by computer experiments. The problem we address is referred to as unlabeled detection and is motivated by large sensor network applications, but applications are also foreseen in different fields, including image processing, social sensing, genome research, and molecular communication.
Special Issue: Chemoinformatics Willett, Peter
Molecules (Basel, Switzerland),
04/2016, Volume:
21, Issue:
4
Journal Article
Peer reviewed
Open access
Chemoinformatics techniques were originally developed for the construction and searching of large archives of chemical structures but they were soon applied to problems in drug discovery and are now ...playing an increasingly important role in many additional areas of chemistry. This Special Issue contains seven original research articles and four review articles that provide an introduction to several aspects of this rapidly developing field.
The two title concepts have been evolving rather rapidly, but independent of each other. The Wasserstein barycenter, on one hand, has mostly made its appearance in image processing as it can describe ...a measure of similarity between images. Its minimization might, for example, suggest the best match in image alignment. On the other hand, MMOSPA estimation has been applied largely to multi-target tracking. The Optimal Sub-Pattern Assignment (OSPA) measures the distance between two sets and the Mean OSPA (MOSPA) can be minimized to give the Minimum MOPSA (MMOSPA), which improves MMSE estimation of the target locations when the labeling of the targets in the set is not important. Approximate and exact algorithms have evolved for both Wasserstein barycenters and MMOSPA estimation. Here, we draw connections between the two perspectives and elaborate how they can benefit from each other.
Preamble detection before data transmission is an important module for an underwater communication system, since false detections would bring undesirable consequences in terms of the lifetime and ...coexistence of underwater networks. This paper conducts a thorough investigation of preamble detection in adverse underwater acoustic channels in the presence of various external interference, such as narrowband interference, impulsive noise, partial-band partial-block-duration interference, and chirps from nearby systems-The Gaussian noise model is not sufficient. We propose two novel detection methods based on the inherent sparsity of underwater acoustic channels: The first method declares signal detection when a sparse signal reconstruction is successful, whereas the second method accumulates the correlation coefficients from multiple paths instead of just the strongest path. We study the performance of the proposed methods based on simulations and experimental data sets, where the detection thresholds are empirically obtained. Performance results testify to the clear advantages of the proposed detection methods relative to existing matched-filter based approaches in various interference conditions.
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