Article
Multidisciplinary Sciences
Emily J. Mayhew, Charles J. Arayata, Richard C. Gerkin, Brian K. Lee, Jonathan M. Magill, Lindsey L. Snyder, Kelsie A. Little, Chung Wen Yu, Joel D. Mainland
Summary: In the study of olfaction, a quantitative model is developed to predict whether a molecule is odorous or odorless based on its chemical properties, leading to a significantly higher estimate of the number of possible odorous compounds.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Thomas E. Hadfield, Jack Scantlebury, Charlotte M. Deane
Summary: Many structure-based virtual screening models can accurately distinguish high affinity binders from non-binders, but often exploit ligand-specific biases instead of identifying favorable intermolecular interactions. This study proposes a novel approach for assessing machine learning-based virtual screening models in identifying the functional groups responsible for binding.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Pankaj Tyagi, Anju Sharma, Rahul Semwal, Uma Shanker Tiwary, Pritish Kumar Varadwaj
Summary: This study developed an XGBoost odor prediction model using machine learning technology, which was able to classify smells of odorant molecules. The results showed that the model could predict all seven basic smells with high precision (>99%) and high sensitivity (>99%), and outperformed other models in predicting common odor descriptors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Pharmacology & Pharmacy
Rui Wang, Jian Xu, Rong Yan, Huanbin Liu, Jingxin Zhao, Yuan Xie, Wenbin Deng, Weiping Liao, Yichu Nie
Summary: In this study, a screening and evaluation model for prodrug against IPF has been established using network pharmacology, virtual screening, and machine learning activity prediction. Two potential compounds, Z103080500 and Z104578368, have been identified and shown to effectively reduce collagen levels and inflammation in an IPF mouse model.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Miriana Di Stefano, Salvatore Galati, Gabriella Ortore, Isabella Caligiuri, Flavio Rizzolio, Costanza Ceni, Simone Bertini, Giulia Bononi, Carlotta Granchi, Marco Macchia, Giulio Poli, Tiziano Tuccinardi
Summary: Cyclin-dependent kinase 5 (Cdk5) plays a crucial role in neurodegenerative diseases and cancer, making it an important drug target. Using a virtual screening approach, we discovered two novel Cdk5 inhibitors with promising enzyme inhibitory and antiproliferative activities. These inhibitors can serve as a starting point for the development of potent Cdk5 inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Doris Schicker, Satnam Singh, Jessica Freiherr, Andreas T. T. Grasskamp
Summary: We have developed and implemented a linear classification algorithm called Olfactory Weighted Sum (OWSum) for predicting the odor of molecules. Our approach relies on the structural patterns of the molecules and uses conditional probabilities combined with tf-idf values. In addition to odor prediction, OWSum provides insights into dataset properties and quantitatively assigns structural patterns to odors, allowing chemists to understand underlying interactions. We also introduced descriptor overlap as a metric for quantifying semantic overlap between descriptors, enabling grouping and derivation of higher-level descriptors. This approach significantly enhances our ability to understand and predict molecular features.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Biochemical Research Methods
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dongsheng Cao, Tingjun Hou
Summary: The study found that most generic machine learning-based scoring functions perform poorly in virtual screening and may not be suitable for real virtual screening activities.
Only a few exceptions, such as RFscore-VS trained on specific datasets, showed superiority for most targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Medicinal
Tuomo Kalliokoski
Summary: HASTEN, a software for structure-based virtual screening using machine learning models, showed reasonable performance with a mean recall value of 0.78 for literature data and excellent recall value of 0.95 for in-house data. It is compatible with any docking- and machine learning methodology and freely available online.
MOLECULAR INFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Manan Goel, Rishal Aggarwal, Bhuvanesh Sridharan, Pradeep Kumar Pal, U. Deva Priyakumar
Summary: Drug design involves identifying and designing new molecules that have desirable properties and bind well to target receptors. Traditional methods have limitations, leading researchers to model virtual screening as a search space problem and use machine learning to reduce computational experiments. Generative methods approximate the entire drug-like chemical space and focus on efficient molecule sampling based on specific properties or receptor structures. This review highlights the importance of modern machine learning methods in enhancing sampling capability beyond conventional screening methods and encourages further development in addressing key aspects of drug design.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Biochemical Research Methods
Liangzhen Zheng, Jintao Meng, Kai Jiang, Haidong Lan, Zechen Wang, Mingzhi Lin, Weifeng Li, Hongwei Guo, Yanjie Wei, Yuguang Mu
Summary: This article presents a novel strategy to develop a reliable protein-ligand scoring function by augmenting the traditional scoring function Vina score using a correction term. The experimental results on various benchmarks show that this strategy enhances the prediction abilities for docking and screening tasks, and can be combined with multiple docking applications.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Pharmacology & Pharmacy
Tong Qin, Zihao Zhu, Xiang Simon Wang, Jie Xia, Song Wu
Summary: The authors reviewed various computational methods for representing protein-ligand interfaces and discussed the impact on machine learning model performance. They highlighted the trend of extracting binding features automatically using deep learning, while also noting areas for improvement.
EXPERT OPINION ON DRUG DISCOVERY
(2021)
Article
Biochemistry & Molecular Biology
Elena Rica, Susana Alvarez, Francesc Serratosa
Summary: This paper explores the distance between attributed graphs for analyzing bioactivity dissimilarity, optimizing it by defining transformation costs, and proposing an algorithm to learn these costs. Experimental results demonstrate that with learned costs, the identification of bioactivity similarities in a group of molecules can be improved.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Guo-Li Xiong, Wen-Ling Ye, Chao Shen, Ai-Ping Lu, Ting-Jun Hou, Dong-Sheng Cao
Summary: Scoring functions based on new protein-ligand interaction representations and advanced ML algorithms, such as the energy auxiliary terms learning (EATL) method, outperform classical SFs in terms of ROC and BEDROC, showing comparable performance with other advanced ML-based methods on the diverse subset of Directory of Useful Decoys: Enhanced (DUD-E). This approach demonstrates effectiveness in improving screening power and can be extended to other docking programs and SFs available.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Software Engineering
Marta Robles, Negar Namdarian, Julia Otto, Evelyn Wassiljew, Nassir Navab, Christine Falter-Wagner, Daniel Roth
Summary: Autism, a neurodevelopmental condition characterized by repetitive behaviors and differences in communication and social interaction, poses challenges in everyday life and can lead to depression, unemployment, and addiction. The long waiting time for diagnosis is a crucial issue in supporting and treating autistic individuals. To address this, a virtual reality shopping experience with an embodied agent is proposed for screening Autism Spectrum Disorders. This approach accurately classifies participants based on their behavioral responses, demonstrating its feasibility.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Medicine, General & Internal
Sarvesh Mehta, Manan Goel, U. Deva Priyakumar
Summary: This study proposes an extension to the machine learning framework for multi-objective Bayesian optimization, which can identify over 90% of the most desirable molecules by explicitly calculating all required properties on only 6% of the entire drug library.
FRONTIERS IN MEDICINE
(2022)
Review
Cell Biology
Sudeshna Das Chakraborty, Silke Sachse
Summary: The perception of olfactory signals plays a crucial role in the survival and reproduction of almost all organisms, with many fundamental principles being shared across different animal phyla. The lateral horn in insects, particularly in Drosophila, has been a key center for integrating and processing innate olfactory behavior, garnering increasing attention in recent years. Studies have focused on mapping and characterizing specific cell types in the lateral horn, their functional properties, neurotransmitter profiles, connectivity to partner neurons, and impact on olfactory behavior.
CELL AND TISSUE RESEARCH
(2021)
Editorial Material
Cell Biology
Silke Sachse, Ivan Manzini
CELL AND TISSUE RESEARCH
(2021)
Editorial Material
Mathematical & Computational Biology
John Crimaldi, Hong Lei, Andreas Schaefer, Michael Schmuker, Brian H. Smith, Aaron C. True, Justus V. Verhagen, Jonathan D. Victor
JOURNAL OF COMPUTATIONAL NEUROSCIENCE
(2022)
Review
Behavioral Sciences
Karen Rihani, Silke Sachse
Summary: Inter-individual differences in behavioral responses, anatomy or functional properties of neuronal populations of animals having the same genotype were for a long time disregarded. Recent studies have shown that individuals with the same genotype can have significant differences in their behavioral biases and preferences to olfactory stimuli. This review focuses on olfaction in the vinegar fly Drosophila melanogaster and discusses the factors that might influence individuality with regard to olfactory perception.
FRONTIERS IN BEHAVIORAL NEUROSCIENCE
(2022)
Correction
Infectious Diseases
Florencia Campetella, Rickard Ignell, Rolf Beutel, Bill S. Hansson, Silke Sachse
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Biology
Sudeshna Das Chakraborty, Hetan Chang, Bill S. Hansson, Silke Sachse, Sonia Sen
Summary: This study investigated the transformation and representation of odor information in higher-order neurons of the lateral horn in Drosophila melanogaster. The researchers found that these neurons exhibited reproducible, stereotypic, and odor-specific response patterns. Importantly, the response amplitude of these neurons was positively correlated with innate odor preferences, suggesting that their activity is valence-specific. The study also revealed that the excitatory input to glutamatergic lateral horn neurons primarily came from uniglomerular projection neurons, while odor-specific inhibition was mediated by inhibitory multiglomerular neurons.
Review
Entomology
Devasena Thiagarajan, Silke Sachse
Summary: Insect behaviors provide valuable insights into evolution and organism complexity, and the study of sensory integration that leads to behavior is highly relevant. This review summarizes recent findings on multimodal sensory integration and the resulting behaviors in insects. The sensory systems in insects, including olfaction, vision, and gustation, have a long history of research, and advancements are continuously being made in understanding thermo- and mechano-sensory systems. Specialized senses like hygro- and magneto-reception have also been identified. The combinatorial approach to studying sensory behaviors mimics the real-life environment of insects, and recent advancements have highlighted the importance of multimodal integration in understanding complex insect behaviors. This review focuses on three insect models (honeybees, ants, and flies) and their behaviors, as well as the underlying neuronal mechanisms of sensory integration.
Review
Ecology
Markus Knaden, Peter Anderson, Martin N. Andersson, Sharon R. Hill, Silke Sachse, Mats Sandgren, Marcus C. Stensmyr, Christer Lofstedt, Rickard Ignell, Bill S. Hansson
Summary: Human activities have a significant impact on the chemical communication of insects. This review focuses on the current state of human-induced changes in insect chemical communication, specifically examining fruit flies, mosquitoes, moths, and bark beetles. The authors also present their perspectives on future developments and the need for further research in this area.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biology
Shawn D. Burton, Audrey Brown, Thomas P. Eiting, Isaac A. Youngstrom, Thomas C. Rust, Michael Schmuker, Matt Wachowiak
Summary: Using high-throughput odorant delivery and ultrasensitive imaging, researchers found that in the mouse olfactory system, odorant receptors are narrowly tuned and highly sensitive, responding to their effective odorants at sub-picomolar to nanomolar concentrations. By utilizing a single diagnostic odorant, many odorant receptors can be reliably identified. The response spectra of odorant receptors to multiple odorants can be predicted based on odorant structural features, and odorant receptors sensitive to distinct odorants with common structural features are spatially clustered.
Article
Multidisciplinary Sciences
Devasena Thiagarajan, Franziska Eberl, Daniel Veit, Bill S. Hansson, Markus Knaden, Silke Sachse
Summary: Animals form sensory associations and store them as memories to guide behavioral decisions. In our study using Drosophila melanogaster, we found that bimodal training improved long-lasting olfactory memory but did not enhance short-term olfactory memory.
Review
Neurosciences
Benjamin Fabian, Silke Sachse
Summary: This review recapitulates the establishment and original meaning of plasticity in neuroscience, introduces the basic composition of the insect olfactory system using Drosophila melanogaster as an example, and outlines experience-dependent plasticity effects observed in various insects. The recent advances in the study of experience-dependent plasticity effects in the olfactory system of D. melanogaster are highlighted, along with discussions on common research problems, overcoming methods, and future directions.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
Article
Food Science & Technology
Maike Laura Fischer, Benjamin Fabian, Yannick Pauchet, Natalie Wielsch, Silke Sachse, Andreas Vilcinskas, Heiko Vogel
Summary: Predatory assassin bugs produce venomous saliva that helps them overpower and digest large prey. The venom of the African assassin bug Psytalla horrida has cytotoxic effects, and our study identified several compounds responsible for its toxicity. These compounds target different organisms, with some having antimicrobial activity and others being involved in prey killing. The findings shed light on the complex mechanisms behind predation and antimicrobial defense in assassin bugs.
Editorial Material
Physiology
Sylvia Anton, Silke Sachse, Robert Huber
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ana Depetris-Chauvin, Diego Galagovsky, Ian W. Keesey, Bill S. Hansson, Silke Sachse, Markus Knaden
Summary: Olfaction is important for animals to find food, but little is known about how the olfactory system evolves and influences behavior. This study compared the olfactory systems of five drosophilid species, including Drosophila melanogaster, that inhabit different ecological niches. The researchers identified natural food odorants from each species and established species-specific odorant preferences. Analysis of the antennal lobe structure and odor coding in sensory neurons revealed that genetic distance and habitat occupancy are key factors in the evolution of olfactory receptors, odor coding, and behavior. Interestingly, changes in odor coding among species cannot be explained by evolutionary changes at a single level but rather involve multiple levels of processing.
Article
Biology
Pramit Bandyopadhyay, Silke Sachse
Summary: This review discusses the encoding of odor mixtures in the Drosophila melanogaster olfactory system and provides an overview of recent findings and challenges in this field.
CURRENT OPINION IN INSECT SCIENCE
(2023)