Recent progress on the prospective application of machine learning to structure-based virtual screening

2021 ◽  
Vol 65 ◽  
pp. 28-34
Author(s):  
Ghita Ghislat ◽  
Taufiq Rahman ◽  
Pedro J. Ballester
2020 ◽  
Vol 20 (14) ◽  
pp. 1375-1388 ◽  
Author(s):  
Patnala Ganga Raju Achary

The scientists, and the researchers around the globe generate tremendous amount of information everyday; for instance, so far more than 74 million molecules are registered in Chemical Abstract Services. According to a recent study, at present we have around 1060 molecules, which are classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today. The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’ will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important computational tool in the drug discovery process; however, experimental verification of the drugs also equally important for the drug development process. The quantitative structure-activity relationship (QSAR) analysis is one of the machine learning technique, which is extensively used in VS techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate. The QSAR model building involves (i) chemo-genomics data collection from a database or literature (ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship (model) between biological activity and the selected descriptors (iv) application of QSAR model to predict the biological property for the molecules. All the hits obtained by the VS technique needs to be experimentally verified. The present mini-review highlights: the web-based machine learning tools, the role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery and advantages and challenges of QSAR.


2019 ◽  
Vol 19 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Qihui Wu ◽  
Hanzhong Ke ◽  
Dongli Li ◽  
Qi Wang ◽  
Jiansong Fang ◽  
...  

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.


2018 ◽  
Vol 15 (1) ◽  
pp. 6-28 ◽  
Author(s):  
Javier Pérez-Sianes ◽  
Horacio Pérez-Sánchez ◽  
Fernando Díaz

Background: Automated compound testing is currently the de facto standard method for drug screening, but it has not brought the great increase in the number of new drugs that was expected. Computer- aided compounds search, known as Virtual Screening, has shown the benefits to this field as a complement or even alternative to the robotic drug discovery. There are different methods and approaches to address this problem and most of them are often included in one of the main screening strategies. Machine learning, however, has established itself as a virtual screening methodology in its own right and it may grow in popularity with the new trends on artificial intelligence. Objective: This paper will attempt to provide a comprehensive and structured review that collects the most important proposals made so far in this area of research. Particular attention is given to some recent developments carried out in the machine learning field: the deep learning approach, which is pointed out as a future key player in the virtual screening landscape.


2016 ◽  
Vol 11 (4) ◽  
pp. 408-420 ◽  
Author(s):  
Cândida G. Silva ◽  
Carlos J.V. Simoes ◽  
Pedro Carreiras ◽  
Rui M.M. Brito

Author(s):  
Siwei Song ◽  
Fang Chen ◽  
Yi Wang ◽  
Kangcai Wang ◽  
Mi Yan ◽  
...  

With the growth of chemical data, computation power and algorithms, machine learning-assisted high-throughput virtual screening (ML-assisted HTVS) is revolutionizing the research paradigm of new materials. Herein, a combined ML-assisted HTVS...


2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Maciej Wójcikowski ◽  
Pedro J. Ballester ◽  
Pawel Siedlecki

Author(s):  
Joel Ricci-Lopez ◽  
Sergio A. Aguila ◽  
Michael K. Gilson ◽  
Carlos A. Brizuela

2018 ◽  
Vol 14 (4) ◽  
pp. 734-747 ◽  
Author(s):  
Constance de Saint Laurent

There has been much hype, over the past few years, about the recent progress of artificial intelligence (AI), especially through machine learning. If one is to believe many of the headlines that have proliferated in the media, as well as in an increasing number of scientific publications, it would seem that AI is now capable of creating and learning in ways that are starting to resemble what humans can do. And so that we should start to hope – or fear – that the creation of fully cognisant machine might be something we will witness in our life time. However, much of these beliefs are based on deep misconceptions about what AI can do, and how. In this paper, I start with a brief introduction to the principles of AI, machine learning, and neural networks, primarily intended for psychologists and social scientists, who often have much to contribute to the debates surrounding AI but lack a clear understanding of what it can currently do and how it works. I then debunk four common myths associated with AI: 1) it can create, 2) it can learn, 3) it is neutral and objective, and 4) it can solve ethically and/or culturally sensitive problems. In a third and last section, I argue that these misconceptions represent four main dangers: 1) avoiding debate, 2) naturalising our biases, 3) deresponsibilising creators and users, and 4) missing out some of the potential uses of machine learning. I finally conclude on the potential benefits of using machine learning in research, and thus on the need to defend machine learning without romanticising what it can actually do.


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