Structure-based virtual screening is an important tool in early stage drug discovery that scores the interactions between a target protein and candidate ligands. As virtual libraries continue to grow ...(in excess of 10
8
molecules), so too do the resources necessary to conduct exhaustive virtual screening campaigns on these libraries. However, Bayesian optimization techniques, previously employed in other scientific discovery problems, can aid in their exploration: a surrogate structure-property relationship model trained on the predicted affinities of a subset of the library can be applied to the remaining library members, allowing the least promising compounds to be excluded from evaluation. In this study, we explore the application of these techniques to computational docking datasets and assess the impact of surrogate model architecture, acquisition function, and acquisition batch size on optimization performance. We observe significant reductions in computational costs; for example, using a directed-message passing neural network we can identify 94.8% or 89.3% of the top-50 000 ligands in a 100M member library after testing only 2.4% of candidate ligands using an upper confidence bound or greedy acquisition strategy, respectively. Such model-guided searches mitigate the increasing computational costs of screening increasingly large virtual libraries and can accelerate high-throughput virtual screening campaigns with applications beyond docking.
Bayesian optimization can accelerate structure-based virtual screening campaigns by minimizing the total number of simulations performed while still identifying the vast majority of computational hits.
Kontrolloitu digitaalinen lainaaminen (Controlled Digital Lending, CDL) on lainauskäytäntö, jonka mukaan elektroninen ja Internetissä toimiva kirjasto voi täysin laillisesti digitoida omistamansa ...kirjan ja lainata digitoitua kappaletta elektronisesti niin, että koko ajan ainoastaan yksi kappale on lainassa tai lainattavissa. Tämän käytännön uranuurtajana on toiminut Internet Archive, mutta se on saanut myös seuraajia, joista tässä artikkelissa esitellään yksi, Digital Theological Library.
Zusammenfassung
Warum eigentlich nicht auch die Bibliotheksmitgliedschaft digitalisieren? Der digitale Bibliotheksausweis des Goethe-Instituts macht Plastikkarten überflüssig und bündelt gleichzeitig ...das digitale Gesamtangebot der Bibliotheken in einer einzigen Anwendung. Konzipiert als mobile Applikation für Android und iOS, ist der digitale Bibliotheksausweis schon an mehr als 50 Bibliotheken des weltweiten Netzwerkes des Goethe-Instituts im Einsatz.
Дигиталне библиотеке као важан сегмент креативне економије добијају све више на значају захваљујући новим и јединственим услугама које пружају на подручју образовних, истраживачких и културних ...потреба. Предмет овог рада је проучавање и анализирање економских аспеката развоја дигиталног библиотекарства. Економска одрживост и избор механизама за покривање трошкова и одређивања цена услуга представљају главне изазове креирања исплативих пословних модела у овој области. За дугорочну економску одрживост дигиталних библиотека нарочито су значајни позитивни ефекти сарадње са другим организацијама, попут заједничког коришћења различитих ресурса као неопходног предуслова за смањење цена услуга и укупних трошкова. Поред тога, у раду је представљено пет основних модела дигиталног библиотечког пословања, као и различити модели финансирања дигиталних библиотека.
Recently, 'tangible' virtual libraries have made billions of molecules readily available. Prioritizing these molecules for synthesis and testing demands computational approaches, such as docking. ...Their success may depend on library diversity, their similarity to bio-like molecules and how receptor fit and artifacts change with library size. We compared a library of 3 million 'in-stock' molecules with billion-plus tangible libraries. The bias toward bio-like molecules in the tangible library decreases 19,000-fold versus those 'in-stock'. Similarly, thousands of high-ranking molecules, including experimental actives, from five ultra-large-library docking campaigns are also dissimilar to bio-like molecules. Meanwhile, better-fitting molecules are found as the library grows, with the score improving log-linearly with library size. Finally, as library size increases, so too do rare molecules that rank artifactually well. Although the nature of these artifacts changes from target to target, the expectation of their occurrence does not, and simple strategies can minimize their impact.
The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, ...we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.
Purpose
The purpose of this paper is to review the literature on factors that contribute to the successful development and use of the mobile digital library (DL). This aim will be achieved by ...reviewing selected journal articles on mobile DLs' successful development and use. This paper argues that the concept of DLs is evolving because of the dynamic nature of knowledge and technological developments in the infosphere.
Design/methodology/approach
A systematic literature search of journal article factors that contribute to the successful development and use of the mobile DL was accomplished by searching the following databases: Emerald insight, Science directory and Google Scholar. The systematic review was conducted following the preferred reporting items for systematic reviews and meta-analyses guidelines. This study applied Rogers's (1965) Diffusion of innovation theory to unpack the attributes of innovation to unpack contextual factors shaping African conceptions of mobile libraries (m-libraries). The studies reviewed were published from 2016 to 2021. This paper is based on a systematic literature review. This paper uses publicly available literature on the theme of DLs concerning m-libraries. Among the search terms used for the study were: “digital libraries”, “Africa and digital libraries”, “electronic libraries”, “information communication technologies”, “access to information” and “mobile digital libraries”.
Findings
Reviewed literature indicates that myriad factors can contribute positively or negatively to the successful development and use of the mobile DL. These factors include the degree of staff awareness and understanding of the potential of mobile technologies in enhancing the provision of library services, the availability of relevant digital content, library staff and users’ level of digital and information literacy competencies to navigate digital platforms, user friendliness of DL platforms, material and financial support to access m-libraries, power supply and access to internet connectivity.
Practical implications
The results from this study will generate knowledge and insight into the factors that affect the development and optimal use of mobile DLs to enhance and widen access to scholarly databases irrespective of time and space. This study will make recommendations that will enable South African policymakers to make informed decisions relating to the factors affecting the development and usage of mobile DLs for enhanced learning, teaching and education.
Originality/value
Given the growing number of scholarly publications on mobile DLs, this study seeks to discover how such technologies can help enhance learning, teaching and research in higher education. This study’s findings will provide a scientific basis for policymakers and researchers with evidence-based knowledge that raises the value of mobile DLs. It was discovered that if the identified factors are handled well, users can easily access tools, such as databases, electronic journals and online reference tools, and this could improve the quality of teaching and learning.
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