PS-GO parametric protein search engine.

With the explosive growth of protein-related data, we are confronted with a critical scientific inquiry: How can we effectively retrieve, compare, and profoundly comprehend these protein structures to maximize the utilization of such data resources? PS-GO, a parametric protein search engine, has been specifically designed and developed to maximize the utilization of the rapidly growing volume of protein-related data. This innovative tool addresses the critical need for effective retrieval, comparison, and deep understanding of protein structures. By integrating computational biology, bioinformatics, and data science, PS-GO is capable of managing large-scale data and accurately predicting and comparing protein structures and functions. The engine is built upon the concept of parametric protein design, a computer-aided method that adjusts and optimizes protein structures and sequences to achieve desired biological functions and structural stability. PS-GO utilizes key parameters such as amino acid sequence, side chain angle, and solvent accessibility, which have a significant influence on protein structure and function. Additionally, PS-GO leverages computable parameters, derived computationally, which are crucial for understanding and predicting protein behavior. The development of PS-GO underscores the potential of parametric protein design in a variety of applications, including enhancing enzyme activity, improving antibody affinity, and designing novel functional proteins. This advancement not only provides a robust theoretical foundation for the field of protein engineering and biotechnology but also offers practical guidelines for future progress in this domain.

PROFASA-a web-based protein fragment and structure analysis workstation.

Introduction: In the field of bioinformatics and computational biology, protein structure modelling and analysis is a crucial aspect. However, most existing tools require a high degree of technical expertise and lack a user-friendly interface. To address this problem, we developed a protein workstation called PROFASA. Methods: PROFASA is an innovative protein workstation that combines state-of-the-art protein structure visualisation techniques with cutting-edge tools and algorithms for protein analysis. Our goal is to provide users with a comprehensive platform for all protein sequence and structure analyses. PROFASA is designed with the idea of simplifying complex protein analysis workflows into one-click operations, while providing powerful customisation options to meet the needs of professional users. Results: PROFASA provides a one-stop solution that enables users to perform protein structure evaluation, parametric analysis and protein visualisation. Users can use I-TASSER or AlphaFold2 to construct protein models with one click, generate new protein sequences, models, and calculate protein parameters. In addition, PROFASA offers features such as real-time collaboration, note sharing, and shared projects, making it an ideal tool for researchers and teaching professionals. Discussion: PROFASA's innovation lies in its user-friendly interface and one-stop solution. It not only lowers the barrier to entry for protein computation, analysis and visualisation tools, but also opens up new possibilities for protein research and education. We expect PROFASA to advance the study of protein design and engineering and open up new research areas.

Thyroid, Gonadal and Adrenal Dysfunction in Kidney Transplant Recipients: A Review for the Clinician.

While chronic kidney disease-associated mineral and bone disorders (CKD-MBD) prevail in the endocrinological assessment of CKD patients, other endocrine abnormalities are usually overlooked. CKD is associated with significant thyroid, adrenal and gonadal dysfunction, while persistent and de novo endocrinological abnormalities are frequent among kidney transplant recipients (KTR). Low T3 levels prior to transplantation may help identify those at risk for delayed graft function and are often found in KTR. Thyroid surveillance after kidney transplantation should be considered due to structural anomalies that may occur. Despite the rapid recovery of gonadal hormonal secretion after renal transplantation, fertility is not completely restored. Testosterone may improve anemia and general symptoms in KTR with persistent hypogonadism. Female KTR may still experience abnormal uterine bleeding, for which estroprogestative administration may be beneficial. Glucocorticoid administration suppresses the hypothalamic-pituitary-adrenal axis in KTR, leading to metabolic syndrome. Patients should be informed about signs and symptoms of hypoadrenalism that may occur after glucocorticoid withdrawal, prompting adrenal function assessment. Clinicians should be more aware of the endocrine abnormalities experienced by their KTR patients, as these may significantly impact the quality of life. In clinical practice, awareness of the specific endocrine dysfunctions experienced by KTR patients ensures the correct management of these complications in a multidisciplinary team, while avoiding unnecessary treatment.

An Overview of Alphafold's Breakthrough.

This paper presents a short summary of the protein folding problem, what it is and why it is significant. Introduces the CASP competition and how accuracy is measured. Looks at different approaches for solving the problem followed by a review of the current breakthroughs in the field introduced by AlphaFold 1 and AlphaFold 2.