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24 Results Found

  • Article
  • Open Access
6 Citations
3,126 Views
14 Pages

Assessing the Utility of ColabFold and AlphaMissense in Determining Missense Variant Pathogenicity for Congenital Myasthenic Syndromes

  • Finlay Ryan-Phillips,
  • Leighann Henehan,
  • Sithara Ramdas,
  • Jacqueline Palace and ,
  • David Beeson and
  • Yin Yao Dong
  • + 1 author+ 0 author

Background/Objectives: Congenital myasthenic syndromes (CMSs) are caused by variants in >30 genes with increasing numbers of variants of unknown significance (VUS) discovered by next-generation sequencing. Establishing VUS pathogenicity requires i...

(This article belongs to the Section Molecular Genetics and Genetic Diseases)
  • Perspective
  • Open Access
12 Citations
4,670 Views
22 Pages

A Model of the Full-Length Cytokinin Receptor: New Insights and Prospects

  • Dmitry V. Arkhipov,
  • Sergey N. Lomin and
  • Georgy A. Romanov

Cytokinins (CK) are one of the most important classes of phytohormones that regulate a wide range of processes in plants. A CK receptor, a sensor hybrid histidine kinase, was discovered more than 20 years ago, but the structural basis for its signali...

(This article belongs to the Special Issue Phytohormones: Important Participators in Plant Growth and Development: 2nd Edition)
  • Article
  • Open Access
7 Citations
2,726 Views
14 Pages

Conservation of Three-Dimensional Structure of Lepidoptera and Trichoptera L-Fibroins for 290 Million Years

  • Russell J. Stewart,
  • Paul B. Frandsen,
  • Steffen U. Pauls and
  • Jacqueline Heckenhauer

13 September 2022

The divergence of sister orders Trichoptera (caddisflies) and Lepidoptera (moths and butterflies) from a silk-spinning ancestor occurred around 290 million years ago. Trichoptera larvae are mainly aquatic, and Lepidoptera larvae are almost entirely t...

(This article belongs to the Section Molecular Structure)
  • Article
  • Open Access
1 Citations
1,636 Views
20 Pages

Integrative Neoepitope Discovery in Glioblastoma via HLA Class I Profiling and AlphaFold2-Multimer

  • Raquel Francés,
  • Jenny Bonifacio-Mundaca,
  • Íñigo Casafont,
  • Christophe Desterke and
  • Jorge Mata-Garrido

Background/Objectives: Glioblastoma multiforme (GBM) is an aggressive primary brain tumor with limited therapeutic options. Neoantigen-based immunotherapy offers a promising avenue, but its efficacy primarily depends on the ability of somatic mutatio...

(This article belongs to the Special Issue Advanced Research in Neuroprotection)
  • Article
  • Open Access
40 Citations
16,340 Views
9 Pages

1 November 2023

Two non-redundant, high-quality sets of protein X-ray crystal structures from the Protein Data Bank (room temperature, 288–298 K, and low temperature, 95–105 K) were compared to structural predictions conducted using ColabFold/AlphaFold2....

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)
  • Article
  • Open Access
14 Citations
5,857 Views
14 Pages

31 December 2022

During coronavirus infection, three non-structural proteins, nsp3, nsp4, and nsp6, are of great importance as they induce the formation of double-membrane vesicles where the replication and transcription of viral gRNA takes place, and the interaction...

(This article belongs to the Special Issue Protein Structure Research)
  • Article
  • Open Access
3 Citations
5,062 Views
11 Pages

12 August 2023

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. The enzymes that install the post-translational modifications on these pep...

(This article belongs to the Topic Computer-Based Solutions to Investigate Biological- and Health-Related Problems)
  • Feature Paper
  • Article
  • Open Access
22 Citations
5,870 Views
16 Pages

Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects

  • Amelia Richter,
  • Darcy Sutherland,
  • Hossein Ebrahimikondori,
  • Alana Babcock and ,
  • Nathan Louie,
  • Chenkai Li,
  • Lauren Coombe,
  • Diana Lin,
  • René L. Warren and
  • Inanc Birol
  • + 10 authors+ 5 authors

27 November 2022

Antimicrobial peptides (AMPs) are a diverse class of short, often cationic biological molecules that present promising opportunities in the development of new therapeutics to combat antimicrobial resistance. Newly developed in silico methods offer th...

(This article belongs to the Special Issue Peptide-Based Antibiotics: Challenges and Opportunities)
  • Article
  • Open Access
5 Citations
3,671 Views
16 Pages

Cargo Recognition Mechanisms of Yeast Myo2 Revealed by AlphaFold2-Powered Protein Complex Prediction

  • Yong Liu,
  • Lingxuan Li,
  • Cong Yu,
  • Fuxing Zeng and ,
  • Fengfeng Niu and
  • Zhiyi Wei
  • + 1 author+ 0 author

26 July 2022

Myo2, a yeast class V myosin, transports a broad range of organelles and plays important roles in various cellular processes, including cell division in budding yeast. Despite the fact that several structures of Myo2/cargo adaptor complexes have been...

(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
  • Article
  • Open Access
2 Citations
2,617 Views
18 Pages

Pleiotropic Role of Rainbow Trout CXCRs in Response to Disease and Environment: Insights from Transcriptional Signatures and Structure Analysis

  • Zhi-Shuai Hou,
  • Hong-Kui Zhao,
  • Pedro Perdiguero,
  • Meng-Qun Liu and ,
  • Kai-Wen Xiang,
  • Chu Zeng,
  • Zhao Li,
  • Xiao-Dong Yang,
  • Qian Yang and
  • Hai-Shen Wen
  • + 8 authors+ 3 authors

12 March 2024

Chemokines are cytokines with chemoattractant capacities that exert their physiological functions through the binding of chemokine receptors. Thus, chemokine and receptor complexes exert important roles in regulating development and homeostasis durin...

  • Review
  • Open Access
7 Citations
4,807 Views
18 Pages

Exploiting Structural Modelling Tools to Explore Host-Translocated Effector Proteins

  • Sahel Amoozadeh,
  • Jodie Johnston and
  • Claudia-Nicole Meisrimler

30 November 2021

Oomycete and fungal interactions with plants can be neutral, symbiotic or pathogenic with different impact on plant health and fitness. Both fungi and oomycetes can generate so-called effector proteins in order to successfully colonize the host plant...

(This article belongs to the Section Molecular Microbiology)
  • Article
  • Open Access
6 Citations
4,760 Views
20 Pages

In Silico Structural Analysis Exploring Conformational Folding of Protein Variants in Alzheimer’s Disease

  • Evangelos Efraimidis,
  • Marios G. Krokidis,
  • Themis P. Exarchos,
  • Tamas Lazar and
  • Panagiotis Vlamos

31 August 2023

Accurate protein structure prediction using computational methods remains a challenge in molecular biology. Recent advances in AI-powered algorithms provide a transformative effect in solving this problem. Even though AlphaFold’s performance ha...

(This article belongs to the Special Issue Structure, Function and Dynamics in Proteins)
  • Article
  • Open Access
3 Citations
2,626 Views
18 Pages

Computational and Experimental Analyses for Pathogenicity Prediction of ACVRL1 Missense Variants in Hereditary Hemorrhagic Telangiectasia

  • Toru Iwasa,
  • Akihiro Urasaki,
  • Yuki Kakihana,
  • Nami Nagata-Akaho and ,
  • Yukihiro Harada,
  • Soichi Takeda,
  • Teruhisa Kawamura,
  • Isao Shiraishi,
  • Kenichi Kurosaki and
  • Osamu Nakagawa
  • + 7 authors+ 2 authors

29 July 2023

Hereditary hemorrhagic telangiectasia (HHT) is a vascular disease caused by the defects of ALK1/ACVRL1 receptor signaling. In this study, we evaluated 25 recently identified ACVRL1 missense variants using multiple computational pathogenicity classifi...

(This article belongs to the Special Issue Hereditary Hemorrhagic Telangiectasia: Diagnosis and Management—Part II)
  • Article
  • Open Access
4 Citations
2,868 Views
16 Pages

Structural Basis for the Interaction between the Ezrin FERM-Domain and Human Aquaporins

  • Helin Strandberg,
  • Carl Johan Hagströmer,
  • Balder Werin,
  • Markus Wendler and ,
  • Urban Johanson and
  • Susanna Törnroth-Horsefield
  • + 1 author+ 0 author

The Ezrin/Radixin/Moesin (ERM) family of proteins act as cross-linkers between the plasma membrane and the actin cytoskeleton. This mechanism plays an essential role in processes related to membrane remodeling and organization, such as cell polarizat...

(This article belongs to the Special Issue New Insights into Aquaporins)
  • Review
  • Open Access
3 Citations
2,285 Views
21 Pages

From Traditional Use to Molecular Mechanisms: A Bioinformatic and Pharmacological Review of the Genus Kalanchoe with In Silico Evidence

  • Cristián Raziel Delgado-González,
  • Ashutosh Sharma,
  • Margarita Islas-Pelcastre,
  • Mariana Saucedo-García and ,
  • Eliazar Aquino-Torres,
  • Jaime Pacheco-Trejo,
  • Silvia Armenta-Jaime,
  • Nallely Rivero-Pérez and
  • Alfredo Madariaga-Navarrete
  • + 4 authors+ 0 author

12 December 2025

The genus Kalanchoe (Crassulaceae) comprises approximately 125 species of succulents distributed across Madagascar, Africa, Arabia, Australia, Southeast Asia, and tropical America. Traditionally regarded as “miracle plants”, Kalanchoe spe...

(This article belongs to the Topic From Plant to Pharmacology: Understanding the Metabolism of Natural Products)
  • Article
  • Open Access
1,889 Views
32 Pages

21 January 2026

CRISPR-Cas9 systems have enabled unprecedented advances in genome engineering, particularly in developing treatments for human diseases, like cancer. Despite potential applications, limitations of Cas9 include its relatively large size and strict tar...

(This article belongs to the Section Molecular Oncology)
  • Article
  • Open Access
1 Citations
1,752 Views
18 Pages

Genomic Characterization of a Rare K30-ST198 Hypervirulent Klebsiella pneumoniae Clone with Distinctive Virulence Features

  • Domingo Fernández Vecilla,
  • Jorge Rodríguez Grande,
  • Nuria Fraile Valcárcel,
  • Mary Paz Roche Matheus and ,
  • Gotzon Iglesias Hidalgo,
  • Cristina Aspichueta Vivanco,
  • José Luis Díaz de Tuesta del Arco,
  • Sergio García-Fernández,
  • María Siller Ruiz and
  • Alain A. Ocampo-Sosa
  • + 11 authors+ 6 authors

1 October 2025

Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a significant public health concern, yet rare sublineages remain poorly characterized. Here, we described a K30-ST198 hvKp sublineage identified in four isolates from two patients, including t...

(This article belongs to the Collection Microbial Virulence Factors)
  • Article
  • Open Access
1 Citations
2,726 Views
20 Pages

Transcriptomic and In Silico Analysis of Microplastic–Protein Interactions in the Tropical Krill Euphausia distinguenda

  • Dulce Estefanía Nicolás-Álvarez,
  • Ricardo Aguilar-Garay,
  • Jorge Alberto Mendoza-Pérez,
  • Jeimy Denisse Santiago-Valentín and
  • Eva R. Kozak

Microplastics (MPs) are pervasive in marine ecosystems, yet the molecular mechanisms underlying their sublethal effects on zooplankton remain poorly understood. Here, we integrated transcriptomic screening with sequence homology analysis, structural...

  • Article
  • Open Access
2 Citations
4,253 Views
16 Pages

15 January 2025

Prion diseases are fatal neurodegenerative diseases that can be transmitted by infectious protein particles, PrPScs, encoded by the endogenous prion protein gene (PRNP). The origin of prion seeds is unclear, especially in non-human hosts, and this id...

(This article belongs to the Section Veterinary Clinical Studies)
  • Article
  • Open Access
3 Citations
2,318 Views
17 Pages

Molecular Dynamics Insights into Peptide-Based Tetrodotoxin Delivery Nanostructures

  • Shenghan Song,
  • Xinyu Xia,
  • Temair Shorty,
  • Tongtong Li and ,
  • Amy O. Stevens,
  • Chao Zhao and
  • Yi He
  • + 2 authors+ 0 author

27 December 2024

Tetrodotoxin (TTX), a potent Site-1 sodium channel blocker (S1SCB), offers highly effective local anesthetic properties with minimal addiction potential. To fully leverage TTX’s capabilities as a local anesthetic, it is crucial to develop a dru...

  • Article
  • Open Access
404 Views
25 Pages

Integrative Genomic and Structure-Based Prioritization of Molecular Targets in Multidrug-Resistant Salmonella enterica from Brazilian Poultry

  • Juan Philippe Teixeira,
  • Daniel Ferreira de Lima Neto,
  • Chiara Ascencio Brancalion,
  • Miklos Maximiliano Bajay and ,
  • Pedro Filipe de Souza Teles,
  • Rafael Straus de Sá,
  • Saad Khan,
  • Thales Quedi Furian and
  • Lenita de Cássia Moura Stefani
  • + 4 authors+ 0 author

Background/Objectives: Multidrug-resistant Salmonella enterica in poultry production poses a persistent challenge for antimicrobial stewardship and food safety. This study integrated phenotypic susceptibility testing, whole-genome sequencing, structu...

(This article belongs to the Topic New Approaches to Machine Learning Parameters in Pharmacology and Pharmacotherapy for Drug Targeting and Precision Medicine)
  • Case Report
  • Open Access
2,573 Views
9 Pages

Clinical and Molecular Traits of a Novel SPECC1L-ALK Fusion in a Patient with Advanced Non-Small Cell Lung Cancer

  • Antonella Centonza,
  • Tommaso Mazza,
  • Domenico Trombetta,
  • Angelo Sparaneo and ,
  • Francesco Petrizzelli,
  • Stefano Castellana,
  • Flavia Centra,
  • Federico Pio Fabrizio,
  • Concetta Martina Di Micco and
  • Lucia Anna Muscarella
  • + 10 authors+ 5 authors

21 June 2024

Anaplastic lymphoma kinase (ALK) fusions account for 5–7% of non-small cell lung cancer (NSCLC) patients, the therapeutic approaches for which have significantly evolved in the last few years. However, the response to target therapies remains h...

(This article belongs to the Special Issue Pathology and Molecular Diagnostics in the Personalized Treatment of Lung Diseases)
  • Article
  • Open Access
2 Citations
2,292 Views
21 Pages

Genomic Insights into Candidozyma auris Clade II: Comparative Phylogenomics and Structural Validation of Fluconazole Resistance Mechanisms

  • Sanghak Lee,
  • Kei-Anne Garcia Baritugo,
  • Han-Soo Kim,
  • Hyeyoung Lee and ,
  • Sook Won Ryu,
  • Soo-Young Kim,
  • Chae Hoon Lee,
  • Young Ree Kim,
  • Jeong Hwan Shin and
  • Gi-Ho Sung
  • + 6 authors+ 1 author

20 January 2026

Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen with confirmed cases in over 30 countries. Although whole-genome sequencing (WGS) analysis defined distinct clades during characterization of underlying gen...

(This article belongs to the Special Issue Mycological Research in South Korea)
  • Article
  • Open Access
1 Citations
2,581 Views
31 Pages

11 October 2023

Transmembrane carriers of the Slc11 family catalyze proton (H+)-dependent uptake of divalent metal ions (Me2+) such as manganese and iron—vital elements coveted during infection. The Slc11 mechanism of high-affinity Me2+ cell import is selectiv...

(This article belongs to the Special Issue Antimicrobial Materials and Nanoparticles)