Article
Biochemistry & Molecular Biology
Aleksandr Sverzhinsky, Alan E. Tomkinson, John M. Pascal
Summary: In this study, the researchers used single-particle cryoelectron microscopy to analyze the complex formed by an archaeal DNA ligase, heterotrimeric PCNA, and single-strand DNA break. The cryo-EM structures revealed a continuous DNA-binding surface between DNA ligase and PCNA, supporting the distorted conformation of the repairing DNA break and contributing to the stimulation of DNA ligation by PCNA. The study also provided insights into the conformational flexibility of DNA ligase within the complex, as well as the potential role of DNA ligase domains in regulating PCNA accessibility to other repair factors.
Article
Biochemistry & Molecular Biology
Michael Silk, Douglas E. Pires, Carlos H. M. Rodrigues, Elston N. D'Souza, Moshe Olshansky, Natalie Thorne, David B. Ascher
Summary: The study introduces a new method that combines sequence- and spatial-based scores to accurately identify pathogenic variants in the human genome, providing a valuable tool for large-scale analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Construction & Building Technology
Sanja Dubljevic, Bojan Tepavcevic, Branko Markoski, Aleksandar S. Andelkovic
Summary: This paper describes a novel computational tool that automates the verification of specific LEED credits in a familiar work environment for architects and engineers. Designers can have real-time visibility of LEED credits achievement at any phase of the design process. The presented method also allows for further elaboration on other LEED credits and research in other green rating certification programs.
ENERGY AND BUILDINGS
(2023)
Article
Biochemical Research Methods
Xifang Sun, Donglin Wang, Jiaqiang Zhu, Shiquan Sun
Summary: In this paper, a completely nonparametric, statistically straightforward, and interpretable method for detecting differentially methylated regions (DMR) is proposed. Compared with existing methods, this method does not rely on model assumptions and is easy to implement, making it a competitive alternative for defining DMR.
BMC BIOINFORMATICS
(2022)
Review
Pharmacology & Pharmacy
Christian Dahlstroem, Themistoklis Paraschiakos, Han Sun, Sabine Windhorst
Summary: Cellular actin dynamics is regulated by various actin binding proteins (ABPs), including nucleating, bundling, cross-linking, capping, and severing proteins. This review focuses on the regulation of actin dynamics by ABPs, with a specific emphasis on the role of cofilin-1, an F-actin severing protein, and L-plastin, an F-actin bundling protein. As the up-regulation of these proteins in cancer is associated with malignant progression, the cryo-EM structure of F-actin with the respective ABP could be used as a template for in silico drug design to disrupt their interaction.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Sergey Margasyuk, Lev Zavileyskiy, Changchang Cao, Dmitri Pervouchine
Summary: RNA structure plays a critical role in the biogenesis and turnover of transcripts. An innovative computational pipeline called PHRIC has been developed to predict long-range RNA structures beyond conserved regions. Application to human cell lines revealed thousands of stable RNA structures with sequence conservation and compensatory substitution patterns.
Article
Biology
Taraneh Zarin, Bob Strome, Gang Peng, Iva Pritisanac, Julie D. Forman-Kay, Alan M. Moses
Summary: This study aims to utilize molecular features within the intrinsically disordered regions (IDRs) of proteins to predict specific biological functions and identify associated features. The results show diverse predictable functions, with some features consistent with previous reports and others previously unknown. Feature analysis represents a new systematic approach to understanding how biological functions of IDRs are determined by their protein sequences.
Article
Genetics & Heredity
Nomaswazi N. N. Maseko, Emma T. T. Steenkamp, Brenda D. D. Wingfield, P. Markus Wilken
Summary: Transcriptional regulation controls gene expression through conserved sequence motifs in regulatory promoter regions. In silico approaches have been used in the study of yeasts and other fungi to identify and characterize these motifs. This study aimed to determine whether in silico approaches could be used to identify motifs in the Ceratocystidaceae family and evaluate their correspondence to known transcription factors. The results showed that in silico approaches could successfully identify known regulatory motifs in the Ceratocystidaceae and unrelated species, supporting ongoing efforts in motif discovery through in silico analyses.
Article
Biochemistry & Molecular Biology
Rahul Kaushik, Kam Y. J. Zhang
Summary: The structural information of proteins plays a crucial role in understanding their functions and interactions. The protein structure prediction method ProFitFun-Meta combines various structural information to assess the quality of predicted model structures. It has been validated and benchmarked against current state-of-the-art methods, demonstrating its reliability and efficiency. ProFitFun-Meta has the potential to become an integral component of computational pipelines for protein modeling and design.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Physical
Aditya Nandy, Michael G. Taylor, Heather J. Kulik
Summary: We surveyed a large number of crystallized mononuclear transition metal complexes to analyze trends in geometric structure and metal coordination. While an increased electron filling generally correlates with a lower coordination number preference, there are exceptions. We also found underrepresentation of 4d/5d transition metals and 3p-coordinating ligands. Among the octahedral complexes, analysis of their ligand environments revealed the presence of removable monodentate ligands, creating reactive sites amenable to catalysis. By analyzing tetradentate ligands, we identified potential catalysts that co-occur with labile monodentate ligands in crystallized complexes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Supatcha Sassanarakkit, Paleerath Peerapen, Visith Thongboonkerd
Summary: A freely accessible web-based tool called OxaBIND has been developed to identify oxalate-binding sites in proteins of interest. This tool provides detailed information about all identified oxalate-binding sites and displays the theoretical three-dimensional structure of the protein with the highlighted oxalate-binding sites. This tool is important for researching the role of oxalate-binding proteins in oxalate-related disorders.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Engineering, Biomedical
Mark C. Allenby, Ee Shern Liang, James Harvey, Maria A. Woodruff, Marita Prior, Craig D. Winter, David Alonso-Caneiro
Summary: Unruptured intracranial aneurysms are common neurovascular anomalies that can lead to catastrophic bleeding. While surgical management can reduce the risk of rupture, traditional methods rely on manual radiological review, but new computer-aided diagnoses may offer more accurate detection.
COMPUTERIZED MEDICAL IMAGING AND GRAPHICS
(2021)
Article
Biochemistry & Molecular Biology
Denis V. Petrovskiy, Kirill S. Nikolsky, Vladimir R. Rudnev, Liudmila I. Kulikova, Tatiana V. Butkova, Kristina A. Malsagova, Arthur T. Kopylov, Anna L. Kaysheva
Summary: This article introduces a new tool called SAFoldNet, which uses neural networks to search and align protein structures. The study shows that this method is competitive in searching and aligning protein structures, and a user-friendly web interface service has been developed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemical Research Methods
Xiaohui Shi, Huajing Teng, Zhongsheng Sun
Summary: This article provides an updated overview of the conformation, current sequencing technologies, and computational identification methods for non-canonical nucleic acid structures, as well as their roles in related biological processes and diseases.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Geography
Jialin Li, Ningchuan Xiao
Summary: This article explores the use of artificial intelligence and machine learning methods in understanding maps, specifically in tasks such as map identification, geographic region recognition, and projection recognition. The results show that pretrained CNN models achieve the highest performance, with an accuracy rate above 90%. However, the performance may decline when tested with systematically distorted maps, indicating both promises and limitations of the current machine learning approaches to cartographic recognition.
ANNALS OF THE AMERICAN ASSOCIATION OF GEOGRAPHERS
(2023)
Article
Biochemical Research Methods
Axel T. Brunger, Debanu Das, Ashley M. Deacon, Joanna Grant, Thomas C. Terwilliger, Randy J. Read, Paul D. Adams, Michael Levitt, Gunnar F. Schroeder
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Abraham O. Samson, Michael Levitt
Article
Biophysics
Jenelle K. Bray, Dahlia R. Weiss, Michael Levitt
BIOPHYSICAL JOURNAL
(2011)
Article
Biochemistry & Molecular Biology
Yao Cong, Gunnar F. Schroeder, Anne S. Meyer, Joanita Jakana, Boxue Ma, Matthew T. Dougherty, Michael F. Schmid, Stefanie Reissmann, Michael Levitt, Steven L. Ludtke, Judith Frydman, Wah Chiu
Article
Multidisciplinary Sciences
Gaurav Chopra, Michael Levitt
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2011)
Article
Multidisciplinary Sciences
Adelene Y. L. Sim, Michael Levitt, Peter Minary
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Multidisciplinary Sciences
Nir Kalisman, Christopher M. Adams, Michael Levitt
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Biochemistry & Molecular Biology
Sergio Moreno-Hernandez, Michael Levitt
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2012)
Article
Biochemistry & Molecular Biology
Julie Bernauer, Xuhui Huang, Adelene Y. L. Sim, Michael Levitt
Article
Biochemistry & Molecular Biology
Junjie Zhang, Boxue Ma, Frank DiMaio, Nicholai R. Douglas, Lukasz A. Joachimiak, David Baker, Judith Frydman, Michael Levitt, Wah Chiu
Article
Biochemical Research Methods
Adelene Y. L. Sim, Olivier Schwander, Michael Levitt, Julie Bernauer
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2012)
Article
Multidisciplinary Sciences
Ivan S. Ufimtsev, Lior Almagor, William I. Weis, Michael Levitt
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Ivan S. Ufimtsev, Michael Levitt
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemical Research Methods
Joao P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, Joao M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Environmental Sciences
Michael Levitt, Francesco Zonta, John P. A. Ioannidis
Summary: Different modeling approaches were used to calculate excess deaths during the COVID-19 pandemic, and large variations in the number of excess deaths were found across countries. After adjusting for age, it was found that 8 out of 33 high-income countries had no overall excess deaths, there was a deficit in child deaths, and 29.7% of the excess deaths occurred in individuals under 65 years old. Additionally, there were significant differences in excess death estimates between countries like France, Germany, Italy, and Spain.
ENVIRONMENTAL RESEARCH
(2022)