Article
Biochemical Research Methods
Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar
Summary: Access pathways are critical for substrate and product transport in enzymes. A Python3 API called pyCaverDock is introduced to enhance the user experience and facilitate ligand transport analysis. This API simplifies the steps needed to use CaverDock and allows for automation of setup processes.
Article
Biochemical Research Methods
Kliment Olechnovic, Ceslovas Venclovas
Summary: VoroContacts is a versatile tool for computing and analyzing contact surface areas and solvent accessible surface areas for proteins, nucleic acids and their complexes at the atomic resolution, with a highly configurable query interface for flexible analysis.
Article
Biochemistry & Molecular Biology
Ahmed Mohamed, Dharmesh D. Bhuva, Sam Lee, Ning Liu, Chin Wee Tan, Melissa J. Davis
Summary: vissE.Cloud is a webserver for gene-set analysis, offering summarisation and interactive visualisation of GSA results. It allows analysis of gene lists as well as raw single-cell and spatial omics data, making it the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ahmed Mohamed, Michelle M. Hill
Summary: LipidSuite is an end-to-end differential lipidomics data analysis server that provides a step-by-step workflow for preprocessing, exploratory analysis, differential analysis, and enrichment analysis of untargeted and targeted lipidomics datasets. It supports the upload of three lipidomics data formats and allows users to interactively explore data and conduct various analyses.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu
Summary: COMMO is the first web server capable of identifying and analyzing consensus gene functionally related gene modules from different module detection methods. It offers a variety of module detection methods, data sources, and analysis functions, providing a user-friendly solution for precision medicine research.
Article
Biochemical Research Methods
Wei He, Helen Wang, Yanjun Wei, Zhiyun Jiang, Yitao Tang, Yiwen Chen, Han Xu
Summary: This study developed an integrative prediction method GuidePro that prioritizes sgRNAs in protein knockouts by incorporating multiple factors. Tested on independent datasets, GuidePro demonstrated superior performance in predicting phenotypes caused by protein loss-of-function, suggesting its robustness in various applications of CRISPR/Cas9 knockouts.
Article
Biochemistry & Molecular Biology
Gerard Minuesa, Cristina Alsina, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Ivan Dotu
Summary: MoiRNAiFold is a versatile and user-friendly tool for de novo synthetic RNA design, based on Constraint Programming, with the ability to handle multiple design constraints and quality measures, and improve features for RNA regulation control of gene expression. Demonstrated to outperform any previous software in benchmarking structural RNA puzzles from EteRNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
Summary: DAVID, a popular bioinformatics resource system, has undergone updates in 2021, including the rebuilding of the DAVID Gene system, increasing the number of gene-term records for annotation types, adding new annotations, assigning specific subgroups, and adding a species parameter for improved user experience.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Chloe Quignot, Guillaume Postic, Helene Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacon, Jessica Andreani, Pierre Tuffery, Raphael Guerois
Summary: The InterEvDock3 protein docking server utilizes evolutionary constraints to generate structural models of protein assemblies, providing 10 candidate complexes and interface predictions. Three key innovations were implemented to improve model reliability, with server performance validated on large benchmark databases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Fatemeh Sabzian-Molaei, Mohammad Ali Nasiri Khalili, Mohammad Sabzian-Molaei, Hosein Shahsavarani, Alireza Fattah Pour, Ahmad Molaei Rad, Amin Hadi
Summary: This study investigates the interaction between Urtica dioica agglutinin (UDA) and the spike protein receptor-binding domain (RBD) of SARS-CoV-2. The results show that UDA can bind to the RBD and inhibit the attachment of the virus to ACE2 receptor on the host cell. The findings suggest that UDA has the potential to be developed as an effective inhibitor against SARS-CoV-2 infection.
Article
Biochemistry & Molecular Biology
Alexander R. van Vliet, George N. Chiduza, Sarah L. Maslen, Valerie E. Pye, Dhira Joshi, Stefano De Tito, Harold B. J. Jefferies, Evangelos Christodoulou, Chloe Roustan, Emma Punch, Javier H. Hervas, Nicola O'Reilly, J. Mark Skehel, Peter Cherepanov, Sharon A. Tooze
Summary: ATG9A and ATG2A are essential core members of the autophagy machinery. Researchers have identified the molecular details of their interaction and demonstrated their importance for autophagy using structural modeling and functional activity analysis.
Article
Multidisciplinary Sciences
Y-h. Taguchi, Turki Turki
Summary: The study proposes a strategy for integrating multiple gene expression profiles from independent studies without labels or sample matching using unsupervised feature extraction. The strategy is applied to Alzheimer's disease-related gene expression profiles, resulting in the selection of biologically relevant genes. Integrated gene expression profiles can function similarly to prior- and/or transfer-learning strategies in other machine learning applications and reduce computational memory requirements in scRNA-seq.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Pavlos Pavlidis, George M. Spyrou
Summary: This study utilizes global genetic data and public health information to select informative SARS-COV-2 mutations in a more precise way, deepening our understanding of the relationship between viral mutations and virulence, and providing important insights for future virus research.
Article
Chemistry, Analytical
Dominik Kopczynski, Nils Hoffmann, Nina Troppmair, Cristina Coman, Kim Ekroos, Michael R. Kreutz, Gerhard Liebisch, Dominik Schwudke, Robert Ahrends
Summary: Lipid analysis is important for understanding the various functions of lipids, and LipidSpace is a standalone tool that analyzes lipidomes by assessing their structural and quantitative differences. It offers a user-friendly GUI and support for multiple data formats, allowing for reanalysis and merging of datasets, and provides additional discoveries.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Jiawei Wu, Qingrui Liu, Min Li, Jiliang Xu, Chen Wang, Junyin Zhang, Minfeng Xiao, Yannan Bin, Junfeng Xia
Summary: PhaGAA is an online integrated platform for phage genome annotation and analysis. It annotates prophage genomes at DNA and protein levels and provides analytical results. Additionally, it can mine and annotate phage genomes from bacterial genomes or metagenomes. This resource will be valuable for experimental biologists and advance phage synthetic biology research.
Article
Biotechnology & Applied Microbiology
Firdous Abdulwahab, Mohamed Abouelhoda, Rula Abouthuraya, Abumansour Imam, Syed O. Ahmed, Khalid Al Rubeaan, Nada Al Tassan, Basma AlAbdulaziz, Khalid AlAbdulrahman, F. H. Alamer, Anas Alazami, Lina A. Al-Baik, Mohammed Aldahmesh, Hasan Al-Dhekri, Haya AlDusery, Sulaiman Algazlan, Abdulaziz Al-Ghonaium, Mohammed Alhamed, Amal Alhashem, Safa Ahmed Alhissi, Abdulelah AlIssa, Mahmoud D. Aljurf, Fowzan S. Alkuraya, Hisham Alkuraya, Rabab Allam, Imam J. Almasharawi, Agaadir Almoisheer, Abeer AlMostafa, Hamoud Al-Mousa, Saleh Al-Muhsen, Eid A. Almutairy, Noukha Alnader, Dhekra AlNaqeb, A. B. AlOtaibi, Afaf Alotibi, Sarah Al-Qattan, Bandar Al-Saud, Haya Al-Saud, M. Alshammari, Hadeel Alsheikh, Abdulmoneem H. Aisheikh, Ayman Al-Sulaiman, A. S. Altamimi, Hamsa Al-Tayeb, S. M. Alwadaee, B. Al-Younes, Fatima Alzahrani, Shamsa Anazi, Rand Arnaout, Bashiri Fahad, Binamer Yousef, F. S. Binhumaid, Saeed Boholega, Dieter Broering, Martin Burdelski, Mahed Jamil Dasouki, Nduna Francis Dzimiri, Tanziel Elamin, Mohamed El-Kalioby, Hussien Elsiesy, Eissa Faqeih, Tariq Faquih, Samya Hagos, Abdulrahman A. Hagr, Mais Hashem, Abbas Hawwari, Selwa Hazzaa, Niema Ibrahim, Faiqa Imtiaz, Amal Jabr, Rana Kattan, Namik Kaya, Amal Kentab, Dania Khalil, Arif O. Khan, Omnia Khier, Brian Meyer, Jawahir Mohamed, Dorota Monies, Paul N. Muiya, Hatem Murad, E. A. Naim, Tarek Owaidah, Nisha Patel, Khushnooda Ramzan, Musafa A. Salih, Mohammad Shagrani, Ranad Shaheen, Hanan Shamseldin, Sogaty Sameera, Subhani Sameera, Taibah Shazia, Wakil Khalid, M. Salma
Article
Genetics & Heredity
Mohamed Abouelhoda, Turki Sobahy, Mohamed El-Kalioby, Nisha Patel, Hanan Shamseldin, Dorota Monies, Nada Ai-Tassan, Khushnooda Ramzan, Faiqa Imtiaz, Ranad Shaheen, Fowzan S. Alkuraya
GENETICS IN MEDICINE
(2016)
Article
Biochemical Research Methods
Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch
BMC BIOINFORMATICS
(2008)
Article
Biochemical Research Methods
Martin Bader, Mohamed I. Abouelhoda, Enno Ohlebusch
BMC BIOINFORMATICS
(2008)
Article
Biochemical Research Methods
Mohamed El-Kalioby, Mohamed Abouelhoda, Jan Krueger, Robert Giegerich, Alexander Sczyrba, Dennis P. Wall, Peter Tonellato
BMC BIOINFORMATICS
(2012)
Article
Biochemical Research Methods
Mostafa M. Abbas, Mohamed Abouelhoda, Hazem M. Bahig
BMC BIOINFORMATICS
(2012)
Article
Biochemical Research Methods
Mohamed Abouelhoda, Shadi Alaa Issa, Moustafa Ghanem
BMC BIOINFORMATICS
(2012)
Article
Multidisciplinary Sciences
Bashayer Al-Mubarak, Mohamed Abouelhoda, Aisha Omar, Hesham AlDhalaan, Mohammed Aldosari, Michael Nester, Hussain. A. Alshamrani, Mohamed El-Kalioby, Ewa Goljan, Renad Albar, Shazia Subhani, Asma Tahir, Sultana Asfahani, Alaa Eskandrani, Ahmed Almusaiab, Amna Magrashi, Jameela Shinwari, Dorota Monies, Nada Al Tassan
SCIENTIFIC REPORTS
(2017)
Article
Biotechnology & Applied Microbiology
Shadi A. Issa, Romeo Kienzler, Mohamed El-Kalioby, Peter J. Tonellato, Dennis Wall, Remy Bruggmann, Mohamed Abouelhoda
BIOMED RESEARCH INTERNATIONAL
(2013)
Article
Multidisciplinary Sciences
Ewa Goljan, Mohammed Abouelhoda, Mohamed M. ElKalioby, Amjad Jabaan, Nada Alghithi, Brian F. Meyer, Dorota Monies
Summary: This study provides a comprehensive overview of pharmacogenetic variation in the Saudi population. It identifies functional variants in pharmacogenes, particularly in CYP genes, and highlights the high polymorphism of VKORC1 gene in this population. Unique rare variants are also found in the Saudi population.
Proceedings Paper
Biochemical Research Methods
Ahmed Abdullah Ali, Mohamed El-Kalioby, Mohamed Abouelhoda
BIOINFORMATICS AND BIOMEDICAL ENGINEERING (IWBBIO 2015), PT I
(2015)
Article
Mathematics, Applied
Enno Ohlebusch, Mohamed I. Abouelhoda, Kathrin Hockel
JOURNAL OF DISCRETE ALGORITHMS
(2007)
