Article
Immunology
Dmitrii S. Shcherbinin, Vadim K. Karnaukhov, Ivan V. Zvyagin, Dmitriy M. Chudakov, Mikhail Shugay
Summary: This study aims to extend and analyze the available structures of TCR-peptide-MHC complexes using highly accurate template-based modeling, providing a methodology to predict TCR specificity.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Ran Liu, Ye-Fan Hu, Jian-Dong Huang, Xiaodan Fan
Summary: A Bayesian model is proposed to jointly infer core locations, binding affinity, and binding thresholds, providing accurate determination for each MHC. Simulation studies showed desirable estimation accuracy and robustness of the model, outperforming commonly used thresholds when applied to real data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Carlos H. M. Rodrigues, Douglas E. Pires, Tom L. Blundell, David B. Ascher
Summary: Protein-protein interfaces have unique binding geometry and physicochemical properties, with concave binding sites that challenge the previous belief about their flatness. A comprehensive review of protein-protein interface landscape reveals the utilization of small binding pockets even in larger flat interfaces.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Chemistry, Medicinal
Aayush Gupta, Huan-Xiang Zhou
Summary: In this study, a machine learning-enabled pipeline was developed for large-scale virtual screening in drug discovery, which successfully conducted clustering and docking screening of compounds, and trained a neural network for classification, bringing breakthroughs to drug discovery research.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Rodrigo Ochoa, Roman A. Laskowski, Janet M. Thornton, Pilar Cossio
Summary: Predicting peptide binders to MHC class II receptors is crucial for autoimmune disease research and vaccine development. This study used simulation interactions to create scoring matrices for estimating binding differences caused by single-point mutations. By optimizing conformation sampling and comparing results to molecular dynamics simulations, the developed scoring-matrix improved performance up to 86% in predicting binding differences.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Dvir Harris, Hila Toporik, Gabriela S. Schlau-Cohen, Yuval Mazor
Summary: The study reveals that photosynthetic supercomplexes exhibit a wide range of conformations but maintain their efficiency due to specific chlorophylls. These protein complexes are essential for converting solar energy with high efficiency. Despite variability in protein organization, the energy transfer efficiency remains consistent. This finding contributes to a better understanding of the mechanism of photosynthesis.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
A. Soldati, J. A. Farrell, R. Wysocki, J. A. Karson
Summary: In ferrovolcanism, metallic lava is denser and less viscous than silicate lava, resulting in faster-moving flows with braided channels. The metallic flow mainly occurs underneath the silicate flow and as breakouts from the silicate flow front, with mingling of the two liquids at the interface.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Alexander J. Bryer, Tyler Reddy, Edward Lyman, Juan R. Perilla
Summary: Enveloped viruses are protected by a lipid membrane, and the complex lipid composition of the envelope is closely related to its structural, mechanical, and dynamical properties.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Quantum Science & Technology
Kaoru Mizuta, Yuya O. Nakagawa, Kosuke Mitarai, Keisuke Fujii
Summary: The LVQC algorithm efficiently compiles time-evolution operators on large-scale quantum systems by optimizing smaller quantum systems, approximating the fidelity of the whole circuit. It is applicable to systems of various dimensions involving finite-, short-, and long-ranged interactions.
Article
Biochemical Research Methods
Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
Summary: In this study, a differential boundary tree-based model, DBTpred, was developed to accurately predict MHC class I binding affinity, outperforming state-of-art deep learning methods. The parallel training algorithm enables DBTpred's application to large datasets, and statistical properties of differential boundary trees provide intuitive interpretation and hints for detecting important residue mutations that influence binding affinity.
Article
Computer Science, Interdisciplinary Applications
Hoon Ryu, Seungmin Lee
Summary: The TB model complements Density Functional Theory for electronic structure simulations of realistically sized nanoscale structures. Efficient utilization of high performance computers can accelerate simulations, and the KNL platform has demonstrated strong scalability and benefits in terms of time and energy consumption.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Physics, Fluids & Plasmas
Bao-quan Ai, Rui-xue Guo
Summary: Research suggests that rigidity disparity alone can drive large-scale demixing in a binary mixture of cell tissues without heterotypic interactions, and there exists an optimal temperature or rigidity disparity for maximum separation in the binary mixture. This separation is possible when the two types of cells exhibit solid-like and liquid-like properties, respectively. The findings also indicate that progenitor cell sorting may occur early in development before robust heterotypic interfacial tensions are established.
Article
Agriculture, Multidisciplinary
Xiaolan Bao, Xingyu Yuan, Guoxue Feng, Meili Zhang, Sarina Ma
Summary: Peptide-Ca complexes can promote calcium absorption, and sunflower seed and peanut peptides have been found to promote calcium transport in Caco-2 cells with characteristic sequences containing glutamic acid and glutamine.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Article
Biochemistry & Molecular Biology
Yifei Wu, Scott D. D. Pegan, David Crich, Lei Lou, Lauren Nicole Mullininx, Edward B. B. Starling, Carson Booth, Andrew Edward Chishom, Kuan Y. Y. Chang, Zhong-Ru Xie
Summary: Papain-like protease (PLpro) plays a critical role in COVID-19 infection and is an important target protein for drug development. Through virtual screening, we identified several drug candidates with convincing binding affinities to the PLpro of SARS-CoV-2. The docking results and analysis showed consistency between the computational approaches and biological experiments, suggesting the potential of these identified compounds for COVID-19 treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Karan Kapoor, Sundar Thangapandian, Emad Tajkhorshid
Summary: Proteins can sample a broad landscape as they undergo conformational transition between different functional states. Considering the different conformational states of a protein is central for a successful drug-design strategy. In this study, a novel docking protocol, termed extended-ensemble docking, is introduced for proteins that undergo large-scale conformational changes. The results show the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.
Article
Medicine, General & Internal
Keira A. Cohen, Tal El-Hay, Kelly L. Wyres, Omer Weissbrod, Vanisha Munsamy, Chen Yanover, Ranit Aharonov, Oded Shaham, Thomas C. Conway, Yaara Goldschmidt, William R. Bishai, Alexander S. Pym
Article
Biochemical Research Methods
Chen Yanover, Natalia Vanetik, Michael Levitt, Rachel Kolodny, Chen Keasar
Article
Hematology
Zuben E. Sauna, Jay N. Lozier, Carol K. Kasper, Chen Yanover, Timothy Nichols, Tom E. Howard
Article
Hematology
S. Saini, N. Hamasaki-Katagiri, G. S. Pandey, C. Yanover, C. Guelcher, V. L. Simhadri, S. Dandekar, M. F. Guerrera, C. Kimchi-Sarfaty, Z. E. Sauna
Editorial Material
Statistics & Probability
Ehud Karavani, Tal El-Hay, Yishai Shimoni, Chen Yanover
STATISTICAL SCIENCE
(2019)
Article
Pharmacology & Pharmacy
Daphna Laifenfeld, Chen Yanover, Michal Ozery-Flato, Oded Shaham, Michal Rosen-Zvi, Nirit Lev, Yaara Goldschmidt, Iris Grossman
Summary: Research utilizing real-world healthcare data has identified two drugs with significant beneficial effects on Parkinson's disease progression, providing insights into potential disease-modifying therapeutic solutions.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Pediatrics
Aneta Gawlik, Anne Salonen, Ching Jian, Chen Yanover, Aleksandra Antosz, Michael Shmoish, Malgorzata Wasniewska, Abdullah Bereket, Stefan A. Wudy, Michaela F. Hartmann, David Thivel, Pawel Matusik, Daniel Weghuber, Ze'ev Hochberg
Summary: The traditional approach to childhood obesity prevention and treatment may not be effective for all patients due to individual variations or misclassifications, highlighting the importance of personalized medicine. High-throughput technologies like next-generation sequencing and metabolomics are valuable tools for providing precise diagnoses and developing personalized treatment approaches. This article also discusses the potential of utilizing omics data to monitor the evolution of symptoms, treatment efficacy, and predisposition to side effects in children with obesity.
Article
Pharmacology & Pharmacy
Grammati Sarri, Dimitri Bennett, Thomas Debray, Anouk Deruaz-Luyet, Montse Soriano Gabarro, Joan A. Largent, Xiaojuan Li, Wei Liu, Jennifer L. Lund, Daniela C. Moga, Mugdha Gokhale, Christopher T. Rentsch, Xuerong Wen, Chen Yanover, Yizhou Ye, Huifeng Yun, Andrew R. Zullo, Kueiyu Joshua Lin
Summary: As the fight against the COVID-19 pandemic continues, there is a growing need for comparative effectiveness research (CER) on preventive and therapeutic interventions. The use of electronic health records (EHRs) provides an opportunity to generate real-world evidence, but there are challenges in ensuring unbiased results. High-quality healthcare databases, rigorous study designs, and proper statistical methods are essential for reliable research.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2022)
Article
Multidisciplinary Sciences
Barak Mizrahi, Maytal Bivas-Benita, Nir Kalkstein, Pinchas Akiva, Chen Yanover, Yoav Yehezkelli, Yoav Kessler, Sharon Hermoni Alon, Eitan Rubin, Gabriel Chodick
Summary: Conducting a second PCR test may help identify patients at risk for severe COVID-19, with early negative results indicating lower risk. This approach is applicable not only to recovering patients but also to those who still have evidence of COVID-19.
SCIENTIFIC REPORTS
(2021)
Review
Public, Environmental & Occupational Health
Richard Wyss, Chen Yanover, Tal El-Hay, Dimitri Bennett, Robert W. Platt, Andrew R. Zullo, Grammati Sari, Xuerong Wen, Yizhou Ye, Hongbo Yuan, Mugdha Gokhale, Elisabetta Patorno, Kueiyu Joshua Lin
Summary: This paper surveys current approaches and recent advancements for high-dimensional proxy confounder adjustment in healthcare database studies, focusing on feature generation, covariate prioritization, selection, and adjustment, as well as diagnostic assessment. While there is a large literature on methods for high-dimensional confounder prioritization/selection, there is relatively little written on best practices for feature generation and diagnostic assessment, indicating particular limitations and challenges in these areas. Machine-learning algorithms are showing promise in supplementing investigator-specified variables to improve confounding control in pharmacoepidemiologic studies, but further research is needed on best practices for feature generation and diagnostic assessment in this context.
PHARMACOEPIDEMIOLOGY AND DRUG SAFETY
(2022)
Article
Health Care Sciences & Services
Michal Ozery-Flato, Yaara Goldschmidt, Oded Shaham, Sivan Ravid, Chen Yanover
Meeting Abstract
Public, Environmental & Occupational Health
Chen Yanover, Karni Marcus, Pini Akiva
PHARMACOEPIDEMIOLOGY AND DRUG SAFETY
(2020)
Article
Public, Environmental & Occupational Health
Chen Yanover, Barak Mizrahi, Nir Kalkstein, Karni Marcus, Pinchas Akiva, Yael Barer, Varda Shalev, Gabriel Chodick
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2020)
Article
Health Care Sciences & Services
Adam Spiro, Jonatan Fernandez Garcia, Chen Yanover
Article
Endocrinology & Metabolism
Assaf Gottlieb, Chen Yanover, Amos Cahan, Yaara Goldschmidt
BMJ OPEN DIABETES RESEARCH & CARE
(2017)