Article
Pharmacology & Pharmacy
Jia-Chen Liu, Sheng-Hua Liu, Guang Fu, Xiao-Rui Qiu, Run-Dong Jiang, Sheng-Yuan Huang, Yong-Li Zhu, Wei-Zheng Li
Summary: This research identified that CD8 + T cells and NK cells were significantly lower in obese individuals, and 11 drugs/compounds were considered to possess obesity-control potential. Furthermore, the expression of drug targets in obese patients were higher than those in controls, suggesting immune cells as potential therapeutic targets for obesity.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Dong Liang, Chen Yu, Zhao Ma, Xingye Yang, Zhenzhen Li, Xuhui Dong, Xiaojun Qin, Lupei Du, Minyong Li
Summary: In this study, we identified parbendazole as a promising compound for the treatment of head and neck squamous cell carcinoma (HNSCC) through a batch query in the connectivity map. Parbendazole was found to inhibit the proliferation of HNSCC cell lines by targeting tubulin and disrupting microtubule polymerization. It demonstrated therapeutic effect and low toxicity in in vivo and in vitro anti-tumor evaluation.
ACTA PHARMACEUTICA SINICA B
(2022)
Article
Computer Science, Information Systems
Lawrence Bai, Madeleine K. D. Scott, Ethan Steinberg, Laurynas Kalesinskas, Aida Habtezion, Nigam H. Shah, Purvesh Khatri
Summary: The study identified atorvastatin as a potential novel therapeutic option for treating UC, demonstrating a significant reduction in colectomy risk. The findings highlight the importance of integrating diverse molecular data with clinical information to repurpose existing FDA-approved drugs for various human diseases at a large scale.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Article
Chemistry, Multidisciplinary
Jessica K. Holien, Lachlan Coff, Andrew J. Guy, Jennifer C. Boer
Summary: During the COVID-19 lockdowns, online learning activities were developed for undergraduate and master's students. An integrative, industry-based research assignment was designed to guide students through a drug discovery project. This assignment allowed students to apply diverse bioinformatic principles to analyze biological and chemical data and make meaningful predictions. It served as the final assessment of the students' knowledge.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Article
Biochemistry & Molecular Biology
Mahdieh Labani, Amin Beheshti, Nigel H. Lovell, Hamid Alinejad-Rokny, Ali Afrasiabi
Summary: KARAJ is a fast and flexible Linux command-line tool for automating the querying and downloading of a wide range of genomic and transcriptomic sequence data types. It can automate four tasks based on input PMCIDs or access numbers, such as providing dataset summaries, calculating file sizes, generating metadata tables, and downloading supplementary data tables. Additionally, it offers a parallel downloading framework powered by Aspera connect to significantly reduce downloading time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Michael R. Lazear
Summary: Given the complexity and volume of proteomics data, efficient software tools for peptide identification and quantification are necessary. This work introduces Sage, a high-performance, open-source, and freely available proteomics pipeline, which matches the performance of state-of-the-art software tools while running significantly faster.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biology
Gerda Cristal Villalba Silva, Thiago Steindorff, Roselena Silvestri Schuh, Natalia Cardoso Flores, Ursula Matte
Summary: This study aimed to identify drugs for treating cardiovascular disease in MPS patients and provided good practices for repositioning analysis. The results suggest that pirfenidone and colchicine are promising drug candidates.
Article
Food Science & Technology
Joseph D. Romano, Hai Li, Tanya Napolitano, Ronald Realubit, Charles Karan, Mande Holford, Nicholas P. Tatonetti
Summary: VenomSeq is a new platform that systematically identifies associations between venoms and drugs/diseases using high-throughput transcriptomics and perturbational differential gene expression analysis. By integrating comparisons to public repositories of differential expression, associations between regulatory networks and disease, and existing knowledge of venom activity, it provides new therapeutic hypotheses linking venoms to human diseases supported by multiple layers of preliminary evidence.
Review
Pharmacology & Pharmacy
Jane F. Armstrong, Brice Campo, Stephen P. H. Alexander, Lauren B. Arendse, Xiu Cheng, Anthony P. Davenport, Elena Faccenda, David A. Fidock, Karla P. Godinez-Macias, Simon D. Harding, Nobutaka Kato, Marcus C. S. Lee, Madeline R. Luth, Ralph Mazitschek, Nimisha Mittal, Jacquin C. Niles, John Okombo, Sabine Ottilie, Charisse Flerida A. Pasaje, Alexandra S. Probst, Mukul Rawat, Frances Rocamora, Tomoyo Sakata-Kato, Christopher Southan, Michael Spedding, Mark A. Tye, Tuo Yang, Na Zhao, Jamie A. Davies
Summary: Anti-malarial drug discovery has traditionally relied on high-throughput phenotypic cellular screening. However, recent advances in understanding druggable targets in the malaria parasite have shifted the focus to target-based approaches. Targeting multiple stages of the parasite lifecycle and linking pharmacological data to specific parasite stages is crucial for developing new anti-malarial medicines. Additionally, the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY provides a valuable web resource for the malaria research community to access published data on malaria pharmacology.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
Jaswanth K. Yella, Anil G. Jegga
Summary: This article introduces a strategy of drug repositioning and predicting new indications using computational methods, and proposes a new approach based on the multi-view graph attention network. This method outperforms four other state-of-the-art methods and demonstrates its potential value in drug discovery through experimental verification.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Psychology, Mathematical
Miguel A. Lago
Summary: Due to the COVID-19 pandemic, researchers are facing challenges in conducting in-person experiments, leading to the exploration of online experimentation. Learning online tools for experimentation can be complex and time-consuming. SimplePhy, a free and open-source tool, aims to simplify the process of programming and hosting experiments for researchers.
BEHAVIOR RESEARCH METHODS
(2021)
Article
Public, Environmental & Occupational Health
Marinella Temprosa, Steven C. Moore, Krista A. Zanetti, Nathan Appel, David Ruggieri, Kaitlyn M. Mazzilli, Kai-ling Chen, Rachel S. Kelly, Jessica A. Lasky-Su, Erikka Loftfield, Kathleen McClain, Brian Park, Laura Trijsburg, Oana A. Zeleznik, Ewy A. Mathe
Summary: COMETS Analytics is a tool developed to support and streamline consortium-based analyses of metabolomics and other -omics data, providing standardized analyses across all cohorts with algorithmic, reproducible approach. It has been shown to scale well and may be useful for facilitating large-scale consortium-based research in metabolomics.
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2022)
Article
Genetics & Heredity
Kejie Li, Jessica Hurt, Christopher D. Whelan, Ravi Challa, Dongdong Lin, Baohong Zhang
Summary: BioInfograph is a web-based tool that allows users to interactively arrange high-resolution images in diversified formats to produce a publication-quality composite figure in both PDF and HTML formats without the need for programming skills. It solves stylesheet conflicts, integrates a rich-text editor, and offers unique interactive HTML output with zoom-in function.
FRONTIERS IN GENETICS
(2022)
Article
Toxicology
F. Jardi, C. Kelly, C. Teague, H. Fowler-Williams, D. C. Sevin, D. Rodrigues, H. Jo, S. Ferreira, B. Herpers, M. Van Heerden, T. de Kok, C. Pin, A. Lynch, C. A. Duckworth, S. De Jonghe, L. Lammens, D. M. Pritchard
Summary: Cross-species comparison of drug responses at the organoid level can help determine the relevance of findings from animal studies in humans. This study evaluated the translatability of preclinical organoids by testing the response of murine intestinal organoids to 5-fluorouracil (5-FU). The results showed that the in vivo gut response to 5-FU was preserved in the organoids, indicating their adequacy in exploring the intestinal response to cytotoxicants.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Biochemical Research Methods
Yingbo Cui, Zihang Wang, Johannes Koester, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Canqun Yang
Summary: VISPR-online is a web-based tool that allows users to visualize, explore, and share CRISPR screening data online. In addition to supporting MAGeCK, it also supports two other popular CRISPR screening analysis tools: BAGEL and JACKS.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Miguel Angel Cuesta-Geijo, Isabel Garcia-Dorival, Ana del Puerto, Jesus Urquiza, Inmaculada Galindo, Lucia Barrado-Gil, Fatima Lasala, Ana Cayuela, Carlos Oscar S. Sorzano, Carmen Gil, Rafael Delgado, Covadonga Alonso
Summary: The inner viral membrane proteins of African swine fever virus (ASFV) interact with endosomal proteins, potentially playing a crucial role in the viral entry process. Silencing or knockout of these proteins affects different stages of ASFV infection, and in some cases, prevents the virus from entering the cytoplasm from endosomes. These findings provide new insights into the role of endosomal proteins in ASFV infection.
Article
Biochemistry & Molecular Biology
R. Sanchez-Garcia, J. R. Macias, C. O. S. Sorzano, J. M. Carazo, J. Segura
Summary: Computational approaches for predicting protein-protein interfaces are important for understanding protein assemblies. The performance of these methods can be improved by selecting specific training datasets. BIPSPI+ is an upgraded version trained on carefully curated datasets, providing better predictions and new functionalities.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
J. Jimenez de la Morena, P. Conesa, Y. C. Fonseca, F. P. de Isidro-Gomez, D. Herreros, E. Fernandez-Gimenez, D. Strelak, E. Moebel, T. O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J. J. Conesa, A. Cuervo, P. Losana, I. Sanchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castano-Diez, A. Koster, J. G. Piccirillo, J. L. Vilas, J. Oton, R. Marabini, C. O. S. Sorzano, J. M. Carazo
Summary: This article introduces the extension of Scipion framework, called ScipionTomo, aiming to simplify image processing and analysis in cryogenic electron tomography. Developed by a collaborative multidisciplinary team, it combines the knowledge of Scipion developers with functionalities requested by beta testers and integrates third-party software packages.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
C. O. S. Sorzano, A. Jimenez-Moreno, D. Maluenda, M. Martinez, E. Ramirez-Aportela, J. Krieger, R. Melero, A. Cuervo, J. Conesa, J. Filipovic, P. Conesa, L. del Cano, Y. C. Fonseca, J. Jimenez-de la Morena, P. Losana, R. Sanchez-Garcia, D. Strelak, E. Fernandez-Gimenez, F. P. de Isidro-Gomez, D. Herreros, J. L. Vilas, R. Marabini, J. M. Carazo
Summary: This article discusses potential problems in cryo-electron microscopy and provides solutions. These problems include sample-related issues and algorithm-related issues. Instabilities in estimating key parameters throughout the processing workflow can significantly affect the reliability of the entire process. The article also proposes a new method to detect parameter bias.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Microbiology
Tiziana Ginex, Clara Marco-Marin, Mitosz Wieczor, Carlos P. Mata, James Krieger, Paula Ruiz-Rodriguez, Maria Luisa Lopez-Redondo, Clara Frances-Gomez, Roberto Melero, Carlos Oscar Sanchez-Sorzano, Marta Martinez, Nadine Gougeard, Alicia Forcada-Nadal, Sara Zamora-Caballero, Roberto Gozalbo-Rovira, Carla Sanz-Frasquet, Rocio Arranz, Jeronimo Bravo, Vicente Rubio, Alberto Marina, Ron Geller, Inaki Comas, Carmen Gil, Mireia Coscolla, Modesto Orozco, Jose Luis Llacer, Jose-Maria Carazo
Summary: This article investigates the impact of the S:A222V mutation on viral infection, and finds that it promotes the opening of RBD and slightly increases ACE2 binding, while not affecting vaccine effectiveness.
Article
Biochemistry & Molecular Biology
Arkadiusz W. Kulczyk, Carlos Oscar S. Sorzano, Przemyslaw Grela, Marek Tchorzewski, Nilgun E. Tumer, Xiao-Ping Li
Summary: This study uses cryo-EM to determine the structure of Shiga toxin 2a (Stx2a) complexed with the ribosomal P-stalk. The findings reveal the dynamics of the Stx2a-P-stalk interaction and suggest that the binding interface between Stx2a and the P-stalk could be a potential target for drug discovery.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
C. O. S. Sorzano, M. A. Perez-de-la-Cruz Moreno, J. L. Vilas
Summary: This article investigates the absorption models of drugs in the body, including carrier mediated transport and saturable absorption. By studying the exact solutions of different absorption models, the differences between these models can be illustrated.
PHARMACEUTICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
D. Herreros, R. R. Lederman, J. M. Krieger, A. Jimenez-Moreno, M. Martinez, D. Myska, D. Strelak, J. Filipovic, C. O. S. Sorzano, J. M. Carazo
Summary: The advancements in Cryo-EM Single Particle Analysis play a vital role in understanding the relationship between macromolecular structure and function in biological processes. Traditional approaches have limitations in fully characterizing the conformational landscape due to the small number of accurately reconstructed states. To overcome this, we propose an extension of the Zernike3D method that can extract continuous flexibility information directly from particle datasets. Additionally, the introduced ZART reconstruction algorithm minimizes blurring induced by molecular motions.
NATURE COMMUNICATIONS
(2023)
Article
Dermatology
Steven D. Rhodes, Frank McCormick, Ross L. Cagan, Annette Bakker, Verena Staedtke, Ina Ly, Matthew R. Steensma, Sang Y. Lee, Carlos G. Romo, Jaishri O. Blakeley, Kavita Y. Sarin
Summary: Cutaneous neurofibromas (cNFs) are the most common tumors in neurofibromatosis type 1 patients, and there is a lack of effective interventions for their treatment. To develop new therapies, it is essential to understand the biology of cNFs, including the role of RAS signaling and downstream pathways. This review provides an overview of the current knowledge on RAS signaling in cNF pathogenesis and therapeutic development.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
D. Herreros, J. Kiska, E. Ramirez-Aportela, J. Filipovic, J. M. Carazo, C. O. S. Sorzano
Summary: The main purpose of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule. ZART is a new Algebraic Reconstruction Technique that can include continuous flexibility information to improve resolution and reduce motion blurring.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Analytical
David Strelak, Daniel Marchan, Jose Maria Carazo, Carlos O. S. Sorzano
Summary: This article conducts a comparative analysis of the quality and performance of commonly used software for movie alignment in Cryo-EM. The tested software includes FlexAlign, MotionCor2, Relion MotionCor, Warp, and CryoSPARC. The alignment precision, power spectra density, and performance scaling were compared using generated phantom data and real datasets.
Article
Biochemistry & Molecular Biology
E. Fernandez-Gimenez, M. M. Martinez, R. Marabini, D. Strelak, R. Sanchez-Garcia, J. M. Carazo, C. O. S. Sorzano
Summary: Single particle analysis is widely used in cryo-electron microscopy to obtain the near-atomic structure of biological macromolecules. However, current projection subtraction methods have limitations in fully removing the signal of components that are not of interest. Therefore, we have developed a new and more precise projection subtraction method, which has shown improved performance compared to existing methods.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Physical
C. O. S. Sorzano, J. L. Vilas, E. Ramirez-Aportela, J. Krieger, D. del Hoyo, D. Herreros, E. Fernandez-Gimenez, D. Marchan, J. R. Macias, I Sanchez, L. del Cano, Y. Fonseca-Reyna, P. Conesa, A. Garcia-Mena, J. Burguet, J. Garcia Condado, J. Mendez Garcia, M. Martinez, A. Munoz-Barrutia, R. Marabini, J. Vargas, J. M. Carazo
Summary: This article proposes a new map validation scheme that takes into account not only the agreement between maps and models, but also factors such as 2D classes, particles, angles, coordinates, defoci, and micrographs. The scheme uses a progressive classification system to qualitatively evaluate the validation status of the results.
FARADAY DISCUSSIONS
(2022)
Article
Biochemistry & Molecular Biology
Dmitry A. Semchonok, Jyotirmoy Mondal, Connor J. Cooper, Katrina Schlum, Meng Li, Muhamed Amin, Carlos O. S. Sorzano, Erney Ramirez-Aportela, Panagiotis L. Kastritis, Egbert J. Boekema, Albert Guskov, Barry D. Bruce
Summary: The tetrameric structure of photosystem I in cyanobacteria has been studied, showing that the tetramer is arranged through two different interfaces. The localization of chlorophyll molecules allows for excitation energy transfer within and between monomers. Tetrameric PSI may play a significant role in the evolution of photosynthetic organisms.
PLANT COMMUNICATIONS
(2022)
