Article
Biochemical Research Methods
Longendri Aguilera-Mendoza, Sebastian Ayala-Ruano, Felix Martinez-Rios, Edgar Chavez, Cesar R. Garcia-Jacas, Carlos A. Brizuela, Yovani Marrero-Ponce
Summary: This article introduces StarPep Toolbox, an open-source software that uses complex network-based representations, clustering, and similarity-searching models to study the bioactive chemical space of antimicrobial peptides (AMPs). The novelty of this research lies in the combination of network science and similarity-searching techniques, distinguishing it from conventional methods based on machine learning and other computational approaches. The network-based representation of the AMP chemical space presents promising opportunities for peptide drug repurposing, development, and optimization, serving as a baseline for the discovery of a new generation of therapeutic peptides.
Article
Engineering, Aerospace
Asma Seddaoui, Chakravarthini M. Saaj
Summary: Future on-orbit servicing and assembly missions require space robots capable of manoeuvring safely. A path generator based on a Genetic Algorithm is designed to take advantage of dynamic coupling effects and controlled motion to safely achieve the target, minimizing objectives and satisfying constraints.
Article
Green & Sustainable Science & Technology
Durgamadhab Swain, Meera Viswavandya, Ritesh Dash, Kalvakurthi Jyotheeswara Reddy, Dhanamjayulu Chittathuru, Arunkumar Gopal, Baseem Khan, Manam Ravindra
Summary: The deployment of a static synchronous compensator can improve voltage and reactive power regulation in a microgrid, enhancing stability and reliability. Coordinating the control system with other distributed energy resources in a microgrid setting can be challenging, necessitating a meticulously designed control system for effective operation.
Article
Nanoscience & Nanotechnology
Chen Wang, Yuan Wang, Weidong Fang, Xiaoxiao Song, Aojie Quan, Michiel Gidts, Hemin Zhang, Huafeng Liu, Jian Bai, Sina Sadeghpour, Michael Kraft
Summary: This paper presents a novel electrostatically actuated microgripper with freeform geometries designed by a genetic algorithm. The microgripper shows improved performance and can handle micro-objects of different sizes. Experimental results confirm the superior performance of this new design methodology.
MICROSYSTEMS & NANOENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Yongbeom Kwon, Juyong Lee
Summary: This study introduces a new molecule optimization method, MolFinder, based on an efficient global optimization algorithm and SMILES representation. MolFinder outperforms other algorithms in optimizing target properties and generating diverse molecules. Its efficiency suggests that combinatorial optimization using SMILES representation is a promising approach, opening up new possibilities for advances in molecule optimization methods.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Phasit Charoenkwan, Nalini Schaduangrat, Pietro Lio, Mohammad Ali Moni, Watshara Shoombuatong, Balachandran Manavalan
Summary: This study introduces a computational tool, SPIDER, for accurate prediction of druggable proteins. By employing various feature descriptors and machine learning algorithms, SPIDER enables more precise and robust prediction compared to baseline models and existing methods in an independent test dataset.
Article
Chemistry, Multidisciplinary
Anna Miller
Summary: The proposed method focuses on tuning a linearized plant model based on real measurements, speeding up the model identification process and improving the model's fit with experimental data. Through reducing standard deviations of model coefficients and eliminating output signal oscillations, the method enhances the mapping of ship dynamics.
APPLIED SCIENCES-BASEL
(2021)
Article
Thermodynamics
Alisan Gonul, Abdulkerim Okbaz, Nurullah Kayaci, Ahmet Selim Dalkilic
Summary: In this study, the effects of delta winglet-type vortex generators on the heat transfer enhancement and pressure loss in microchannels were investigated numerically. It was found that vortex generators significantly improve heat transfer performance with a corresponding increase in pressure loss. Multi-objective optimization and sensitivity analysis were conducted to determine the most optimum design parameters and propose practical correlations for Nusselt number and friction factor.
APPLIED THERMAL ENGINEERING
(2022)
Article
Engineering, Chemical
Yachen Lu, Yufan Teng, Qi Zhang, Jiaquan Dai
Summary: In this paper, a new prediction model is proposed to accurately recognize and evaluate the trends of domestic chemical products and improve the forecasting accuracy of their prices. The model uses the minimum forecasting error as the evaluation objective for forecasting the settlement price. The proposed model utilizes an improved genetic algorithm to optimize the parameters of a long short-term memory (LSTM) network. Experimental results show that the proposed IGA-LSTM model has excellent forecasting performance with minimal forecasting errors for two types of chemical products.
Article
Computer Science, Artificial Intelligence
Llio Humphreys, Guido Boella, Leendert van der Torre, Livio Robaldo, Luigi Di Caro, Sepideh Ghanavati, Robert Muthuri
Summary: This article introduces a semantic role labeling based information extraction system to extract definitions and norms from legislation and represent them as structured norms in legal ontologies. The goal is to make laws more accessible, understandable, and searchable in a legal document management system.
ARTIFICIAL INTELLIGENCE AND LAW
(2021)
Article
Computer Science, Artificial Intelligence
Lanlan Zheng, Xin Liu, Feng Wu, Zijun Zhang
Summary: This paper addresses the two-dimensional shelf space allocation problem (2DSSAP) in the retail field by proposing a data-driven model assisted hybrid genetic algorithm (DMA-HGA). The proposed DMA-HGA applies an improved genetic algorithm (GA) to optimize solutions and a two-stage search assistance module to enhance the search process. Experimental results demonstrate that the DMA-HGA outperforms benchmarking methods in terms of solution quality and accuracy. The extended discussion of parameters also provides valuable management insights for the 2DSSAP.
SWARM AND EVOLUTIONARY COMPUTATION
(2023)
Article
Engineering, Electrical & Electronic
Lei Yang, Kan Wang, Hongbing Sun
Summary: This paper presents a novel parameter design method for phased arrays using genetic algorithm optimization to suppress grating and quantization lobes. By setting normalized values and maximum gaps as optimization variables, the method significantly improves convergence speed and provides strong global optimization capabilities.
IET MICROWAVES ANTENNAS & PROPAGATION
(2022)
Article
Engineering, Geological
Francisco Jose Mendez, Antonio Pasculli, Miguel Alfonso Mendez, Nicola Sciarra
Summary: This article introduces an optimization framework based on genetic algorithms to calibrate the constitutive law of von Wolffersdorff, improving the accuracy of the Sand Hypoplasticity model. By combining the GA with a numerical solver, the complex calibration involving eight parameters can be automatically fitted, allowing for uncertainty quantification and analysis of parameter importance. Testing on synthetic and experimental data shows improved model prediction and calibration.
Article
Computer Science, Artificial Intelligence
Chih-Ching Chang, Che-Chern Lin
Summary: The study presents a genetic algorithm for assigning freshmen's dormitory rooms based on living habits and preferences, which achieved better fitness values through locally exhaustive crossover and half-half selection strategy. Experimental results demonstrated acceptable performances with reasonable computational time.
APPLIED ARTIFICIAL INTELLIGENCE
(2021)
Review
Pharmacology & Pharmacy
Martin Vogt
Summary: This article provides an overview of popular deep learning methods for exploring chemical space. Key aspects such as molecular representation selection, focused training for chemical space exploration, and criteria for evaluating and validating chemical space coverage are discussed.
EXPERT OPINION ON DRUG DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Paris Jafari, Alexandre Luscher, Thissa Siriwardena, Murielle Michetti, Yok-Ai Que, Laurence G. Rahme, Jean-Louis Reymond, Wassim Raffoul, Christian Van Delden, Lee Ann Applegate, Thilo Kohler
Summary: In this article, a novel cell therapy formulation is developed to resist infections and inhibit the virulence pathways of pathogenic bacteria by incorporating antimicrobial peptide dendrimers and anti-quorum sensing compounds. The formulation includes live progenitor cells, exhibiting bactericidal and anti-virulence properties without compromising cell viability.
Article
Chemistry, Medicinal
Elena Zakharova, Markus Orsi, Alice Capecchi, Jean-Louis Reymond
Summary: This study successfully discovered new non-hemolytic anticancer peptides using recurrent neural networks and machine learning methods, demonstrating the first application of machine learning in this field.
Article
Chemistry, Multidisciplinary
Johannes Morstein, Alice Capecchi, Konstantin Hinnah, ByungUk Park, Jerome Petit-Jacques, Reid C. Van Lehn, Jean-Louis Reymond, Dirk Trauner
Summary: Most bioactive molecules need to cross or be distributed into biological membranes, and natural products often have lipid modifications to facilitate molecule-membrane interactions. Lipidated natural products primarily contain saturated medium-chain lipids, and lipid conjugation can significantly modulate the permeability, cellular retention, subcellular localization, and bioactivity of small molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Valentina Rossetti, Jean-Louis Reymond
Summary: In this article, we share the aims, development, challenges, and outcome of the National Center of Competence in Research (NCCR) TransCure's temporary learning and artistic path called 'Vitaport - Was unser Korper transpor-tiert' in Bern. This project involved NCCR TransCure researchers and students from the Bern School of Design, who developed ceramic objects, texts, and information graphics to take the public on a multidisciplinary journey through the human body.
Article
Chemistry, Multidisciplinary
Tin Manh Ho, Stephan Berger, Philipp Mueller, Celine Simonin, Jean-Louis Reymond, Christoph von Ballmoos, Daniel G. Fuster
Summary: The goal of this research was to investigate the physiological and molecular function of NHA2, develop a high resolution kinetic transport assay, and identify specific compounds targeting NHA2. The interdisciplinary and interfaculty effort led to successful results and provided important information for further research and drug development.
Article
Chemistry, Multidisciplinary
Jean-Louis Reymond
Summary: Quantifying molecular similarity is crucial in drug discovery and optimization. This review focuses on computational methods developed in the NCCR TransCure interdisciplinary network for studying physiology, structural biology, and pharmacology of ion channels and membrane transporters. The review highlights the use of molecular similarity measures in scaffold hopping, predicting off-target effects, and creating chemical space maps.
Article
Chemistry, Medicinal
Ye Buehler, Jean-Louis Reymond
Summary: The generated databases (GDBs) list billions of possible molecules through systematic enumeration following simple rules of chemical stability and synthetic feasibility. The originality of GDB molecules can be assessed by comparing their Bemis and Murcko molecular frameworks (MFs) with those in public databases. This comparison revealed that GDB-13s MFs had diverse ring sizes and ring systems without linker bonds, making them attractive targets for synthetic chemistry aiming at innovative molecules.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Joel S. Bloch, Alan John, Runyu Mao, Somnath Mukherjee, Jeremy Boilevin, Rossitza N. Irobalieva, Tamis Darbre, Nichollas E. Scott, Jean-Louis Reymond, Anthony A. Kossiakoff, Ethan D. Goddard-Borger, Kaspar P. Locher
Summary: C-linked glycosylation is essential for the trafficking, folding, and function of secretory and transmembrane proteins involved in cellular communication processes. Cryogenic-electron microscopy structures of Caenorhabditis elegans CMT reveal how the CMT recognizes the glycosylation sequon and triggers conformational activation of the donor substrate, enabling C-glycosylation of proteins. These findings have implications for understanding human diseases and potential therapeutic targeting of specific CMT paralogs.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Hippolyte Personne, Thissa N. Siriwardena, Sacha Javor, Jean-Louis Reymond
Summary: Here, we demonstrate that dipropylamine (DPA) can effectively reduce aspartimide formation in high-temperature solid-phase peptide synthesis (SPPS) compared to piperidine (PPR). DPA is easily accessible, inexpensive, non-toxic, and odorless, making it a promising alternative to PPR. Furthermore, DPA yields good results in SPPS of non-aspartimide-prone peptides and peptide dendrimers.
Article
Chemistry, Multidisciplinary
Etienne Bonvin, Jean-Louis Reymond
Summary: We redesigned the branches of PAMAM dendrimers to improve their stability by modifying the amide carbonyl group. The resulting i-PAMAM dendrimers have the same carbon framework as PAMAMs but differ in the position of the carbonyl group. Compared to PAMAMs, which are difficult to purify, we synthesized i-PAMAMs using solid-phase peptide synthesis and purified them using preparative reverse phase HPLC. Our i-PAMAM dendrimers showed no degradation over time and exhibited potent antimicrobial activities against both Gram-negative and Gram-positive bacteria.
HELVETICA CHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Matheus A. Meirelles, Jean-Louis Reymond
Summary: This study presents an optimized synthesis method for a probe used in studying protein N-glycosylation in eukaryotic cells. The yields and reaction times of three phosphate coupling steps were improved by adjusting reagents and conditions. An efficient purification protocol was also developed to obtain the pure product.
HELVETICA CHIMICA ACTA
(2023)
Article
Chemistry, Medicinal
Ye Buehler, Jean-Louis Reymond
Summary: Identifying novel ring fragments (RFs) and acyclic fragments (AFs) from public databases and natural products can provide potential opportunities for drug innovation in fragment-based drug discovery.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Etienne Bonvin, Hippolyte Personne, Thierry Paschoud, Jeremie Reusser, Bee-Ha Gan, Alexandre Luscher, Thilo Kohler, Christian van Delden, Jean-Louis Reymond
Summary: By introducing peptoid units into antimicrobial peptides, the antimicrobial effects can be retained with reduced toxicity to human cells, and under specific conditions, there may be a transition towards intracellular targeting.
ACS INFECTIOUS DISEASES
(2023)
Article
Chemistry, Multidisciplinary
David Kreutter, Jean-Louis Reymond
Summary: This study introduces a new tool for computer-aided synthesis planning that can automatically learn organic reactivity and perform retrosynthesis. The tool combines a triple transformer loop and a multistep tree search algorithm to propose short synthetic routes based on commercial starting materials.
Article
Chemistry, Multidisciplinary
David Kreutter, Philippe Schwaller, Jean-Louis Reymond
Summary: Training a molecular transformer model with multi-task transfer learning and combining extensive reaction and enzymatic transformation data allows for accurate prediction of the structure and stereochemistry of enzyme-catalyzed reaction products.