For extraction of information on binding sites of a protein, the commonly known geometry-based methods utilize the corresponding PDB file to extract its surface as a first step. Finally, the surface is used to find the binding site atoms. As shown in this paper work, since none of the mostly used surface extraction methods can retrieve a sizeable percentage of the binding site atoms, the scope of development of a better method remains. In this direction, this paper presents a new benchmarking criteria based on utilization of binding site information to compare performance of these surface extraction methods. Also, a new surface extraction method is introduced based on the use of a rotating cylinder probe adapting from the work of Weisel et al. (Chem Cent J 1:7-23, 2007. doi: 10.1186/1752-153X-1-7 ). The result of the new method shows a significant improvement of performance in comparison to the existing methods.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/s12539-016-0201-8 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Assessing the Efficacy of Pyrolysis-Gas Chromatography-Mass Spectrometry for Nanoplastic and Microplastic Analysis in Human Blood.
Environ Sci Technol
January 2025
Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, Queensland 4102, Australia.
Humans are constantly exposed to micro- and nanosized plastics (MNPs); however, there is still limited understanding of their fate within the body, partially due to limitations with current analytical techniques. The current study assessed the appropriateness of pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) analysis for the quantification of a range of polymers in human blood. An extraction protocol that reduced matrix interferences (false positives) of polyethylene (PE) and polyvinyl chloride (PVC) was developed and validated.
View Article and Find Full Text PDFAssociation of individual-based morphological brain network alterations with cognitive impairment in type 2 diabetes mellitus.
Front Neurol
January 2025
Department of Radiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
Objective: To investigate the altered characteristics of cortical morphology and individual-based morphological brain networks in type 2 diabetes mellitus (T2DM), as well as the neural network mechanisms underlying cognitive impairment in T2DM.
Methods: A total of 150 T2DM patients and 130 healthy controls (HCs) were recruited in this study. The study used voxel- and surface-based morphometric analyses to investigate morphological alterations (including gray matter volume, cortical thickness, cortical surface area, and localized gyrus index) in the brains of T2DM patients.
Comparative analysis of LC-HRMS profiling, ATR FT-IR spectroscopy, antioxidant, anti-diabetic, and anti-tyrosinase activities of extracts from Cotoneaster frigidus Wall. Ex Lindl. "Cornubia" fruit.
Food Res Int
February 2025
Karadeniz Technical University, Faculty of Science, Department of Chemistry, Trabzon, Türkiye. Electronic address:
The antioxidant, total phenolic, flavonoid, and anthocyanidin properties of extracts prepared from Cotoneaster frigidus Wall. ex Lindl. "Cornubia" fruit were examined.
View Article and Find Full Text PDFShort dentin etching with universal adhesives: effect on bond strength and gingival margin adaptation.
BMC Oral Health
January 2025
Conservative Department, Faculty of Dentistry, Kafr Al Sheikh University, Kafr Al Sheikh, Egypt.
Background: Short dentin etching, a relatively recent technique, aims to improve resin-dentin bonding by preserving hydroxyapatite crystals within the collagen spaces. This study explores short dentin etching's potential in mitigating over-etching issues in deep proximal dentin/cementum margins, an aspect not previously investigated. This study evaluates the microtensile bond strength (μTBS) and marginal adaptation of two universal adhesives using different etch-and-rinse strategies (15-second and 3-second etching) and self-etch strategies, both immediate and post-thermal cycling and mechanical loading.
View Article and Find Full Text PDFConcentration of Povidone-Iodine Pocket Irrigation in Implant-Based Breast Surgery: A Scoping Review.
Aesthetic Plast Surg
January 2025
Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia.
Background: In implant-based breast surgery, microbial contamination of implant surfaces predisposes complications such as overt periprosthetic infection and has been linked to capsular contracture (CC). Anti-microbial practices, including povidone-iodine (PVP-I) breast pocket irrigation, are routinely employed to minimise these risks. No standardised protocol for using this antiseptic exists, particularly concerning the ideal concentration.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!