A5007118386- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- Computational Drug Discovery Methods
- Protein Interaction Studies and Fluorescence Analysis
- Trace Elements in Health
- Electron and X-Ray Spectroscopy Techniques
- Drug Transport and Resistance Mechanisms
- Nanoparticle-Based Drug Delivery
- thermodynamics and calorimetric analyses
- Machine Learning in Materials Science
- Methane Hydrates and Related Phenomena
- Mass Spectrometry Techniques and Applications
- Hydrocarbon exploration and reservoir analysis
- Metal complexes synthesis and properties
- Lipid Membrane Structure and Behavior
- Corrosion Behavior and Inhibition
- Radiopharmaceutical Chemistry and Applications
- Hemoglobin structure and function
- Advanced Electron Microscopy Techniques and Applications
- Machine Learning in Bioinformatics
- Advanced Materials Characterization Techniques
- Clinical Laboratory Practices and Quality Control
- Lanthanide and Transition Metal Complexes
- RNA modifications and cancer
Jagiellonian University
2021-2025
University of Virginia
2022-2025
Hunan University
2024
First Affiliated Hospital of Shantou University Medical College
2024
Shantou University
2024
Abstract Metal ions bound to macromolecules play an integral role in many cellular processes. They can directly participate catalytic mechanisms or be essential for the structural integrity of proteins and nucleic acids. However, their unique nature make them difficult model refine, a substantial portion metal PDB are misidentified poorly refined. CheckMyMetal (CMM) is validation tool that has gained widespread acceptance as researchers working on metal‐macromolecule complexes. CMM used...
Serum albumin–Co2+ interactions are of clinical importance. They play a role in mediating the physiological effects associated with cobalt toxicity and central to albumin binding (ACB) assay for diagnosis myocardial ischemia. To further understand these processes, deeper understanding is required. Here, we present first crystallographic structures human serum (HSA; three structures) equine (ESA; one structure) complex Co2+. Amongst total sixteen sites bearing ion across structures, two...
Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural, catalytic, or regulatory roles. Modeling transition metal ions, especially transient, reversible, concentration-dependent sites, remains challenging. We present PinMyMetal (PMM), a hybrid machine learning system designed accurately predict localization environment macromolecules, tailored tetrahedral octahedral geometries. PMM outperforms...
Identifying and characterizing metal-binding sites (MBS) within macromolecular structures is imperative for elucidating their biological functions. CheckMyMetal (CMM) a web based tool that facilitates the interactive validation of MBS in determined through X-ray crystallography cryo-electron microscopy (cryo-EM). Recent updates to CMM have significantly enhanced its capability efficiently handle large datasets generated from cryo-EM structural analyses. In this study, we address various...
Abstract Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue or regulatory (2-residue predominate) roles. Computational tools modeling metal structures, especially transient, reversible, concentration-dependent sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system predicting zinc ion localization...
Molecular modeling is an excellent tool for studying biological systems on the atomic scale. Depending objects, which may be proteins, nucleic acids, or lipids, different force fields are recommended. The phospholipid bilayers constitute example, in behavior extensively studied using molecular dynamics simulations due to limitations of experimental methods. reliability results strongly dependent appropriate description these compounds. There some deficiencies parametrization intra- and...
The overall quality of the experimentally determined structures contained in PDB is exceptionally high, mainly due to continuous improvement model building and structural validation programs. Improving reproducibility on a large scale requires expanding concept biology all other disciplines include broader framework that encompasses entire project. A successful approach science diligent attention detail focus future. An earnest commitment data availability reuse essential for scientific...
Over the course of pandemic caused by SARS-CoV-2, structural biologists have worked hand in with groups developing vaccines and treatments. However, relying solely on vitro clinical studies may be insufficient to guide vaccination treatment developments, other healthcare policies during virus mutations or peaks infections fatalities. Therefore, it is crucial track statistical data related number infections, deaths, vaccinations specific regions present an easy-to-understand way.
CheckMyMetal is a server used to validate the metal binding sites of macromolecular structures.An easy-to-use interface allows evaluation structures in PDB or uploaded by user.The new version incorporates electron density maps, which expands number parameters for validation.The structure and maps are now displayed using NGL viewer provide more informative intuitive experience.One most important features ability conduct fast refinement vicinity around alternate candidates.CheckMyMetal guides...
Researchers worldwide from almost every biomedical discipline perform basic searches of the PDB, so essential information in a PDB deposit must be as informative possible.On larger scale, inaccurate or misleading metadata can skew data mining efforts.The title and keywords deposits may play an role PDB.The primary citation (reference) help such search, yet many have notable discrepancies between structure reference title.Moreover, we observed that fraction with status "To published" has...