structure similarity
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2022 ◽  
Author(s):  
Adam Zemla ◽  
Jonathan E. Allen ◽  
Dan Kirshner ◽  
Felice C. Lightstone

We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (spheres) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. Currently, PDBspheres library contains more than 2 million spheres, organized to facilitate searches by sequence and/or structure similarity of protein-ligand binding sites or interfaces between interacting molecules. PDBspheres uses the LGA structure alignment algorithm as the main engine for detecting structure similarities between the protein of interest and library spheres. An all-atom structure similarity metric ensures that sidechain placement is taken into account in the PDBspheres primary assessment of confidence in structural matches. In this paper, we (1) describe the PDBspheres method, (2) demonstrate how PDBspheres can be used to detect and characterize binding sites in protein structures, (3) compare PDBspheres use for binding site prediction with seven other binding site prediction methods using a curated dataset of 2,528 ligand-bound and ligand-free crystal structures, and (4) use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of the 4,876 structures in the refined set of PDBbind 2019 dataset. The PDBspheres library is made publicly available for download at https://proteinmodel.org/AS2TS/PDBspheres


Author(s):  
Calvin Omind Munna

Currently, there a growing demand of data produced and stored in clinical domains. Therefore, for effective dealings of massive sets of data, a fusion methodology needs to be analyzed by considering the algorithmic complexities. For effective minimization of the severance of image content, hence minimizing the capacity to store and communicate data in optimal forms, image processing methodology has to be involved. In that case, in this research, two compression methodologies: lossy compression and lossless compression were utilized for the purpose of compressing images, which maintains the quality of images. Also, a number of sophisticated approaches to enhance the quality of the fused images have been applied. The methodologies have been assessed and various fusion findings have been presented. Lastly, performance parameters were obtained and evaluated with respect to sophisticated approaches. Structure Similarity Index Metric (SSIM), Mean Squared Error (MSE), Peak Signal-to-Noise Ratio (PSNR) are the metrics, which were utilized for the sample clinical pictures. Critical analysis of the measurement parameters shows higher efficiency compared to numerous image processing methods. This research draws understanding to these approaches and enables scientists to choose effective methodologies of a particular application.


2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Rongxin Zhan ◽  
Jinhui Zhang ◽  
Zihua Cui ◽  
Jin Peng ◽  
Dongni Li

In current environments, production systems need the ability of quick response to face the volatile markets. Seru production systems, as a new mode of the production system, have the advantages of quick response, high flexibility, and high efficiency. Seru scheduling, which refers to constructing serus with an exact sequence in limited workspace, is an important decision problem in the operational management of seru production systems and can reflect the reconfiguration nature of seru production systems. This study investigates a seru scheduling problem with resource conflicts, whose objective is to minimize the makespan. An automatic heuristic design approach that combines a genetic programming algorithm and structure similarity-based operators is proposed. Comparative experiments are conducted with human-made rules, basic genetic programming, genetic programming-based algorithm, and with some state-of-the-art scheduling algorithms. The results show the effectiveness and efficiency of the proposed algorithm.


2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Shereen Mowaka ◽  
Nermeen Ashoush ◽  
Mariam M. Tadros ◽  
Bassam M. Ayoub

Trelagliptin (TLN) is a novel once-weekly antidiabetic drug that enhanced the patient compliance in type 2 diabetes. TLN analysis and bioanalysis literature review showed many methods for TLN assay either in dosage form or as biological fluids (pharmacokinetic parameters), but all those methods did not consider the full details dealing with biological assay of TLN. Studies that included information about pharmacokinetic parameters did not mention the used analytical procedures for those determinations and parameters. Although some LC-MS/MS and UPLC-UV methods were reported for TLN bioassay in rats’ plasma, they used direct precipitation techniques, and the current described procedure showed lower LLOQ than all the reported methods in spite of that working on human plasma is more complicated than on rats’ plasma. In this study, LC-MS/MS bioanalysis of TLN in human plasma (4–1000 nM) was employed successfully with LLOQ of 4 nM which is lower than all reported methods in rats’ plasma followed by a preliminary pharmacokinetic study. Alogliptin was used as internal standard (IS) because of its structure similarity to TLN. Pharmacokinetic parameters of TLN were investigated in Egyptian volunteers, and they had been compared to Japanese. Liquid-liquid extraction showed more sensitive results than direct precipitation. The proposed method was successfully applied to a pharmacokinetic study conducted on Egyptian volunteers. No dose modification is required upon comparing the pharmacokinetic parameters of the current study and previous studies on non-Egyptian volunteers.


2021 ◽  
Author(s):  
Saminur Islam ◽  
Ahmed Abbasi ◽  
Nitin Agarwal ◽  
Wanhong Zheng ◽  
Gianfranco Doretto ◽  
...  

2021 ◽  
Author(s):  
Anna M. Bischofberger ◽  
Alex R. Hall

AbstractHumans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae, Staphylococcaceae and Streptococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.


Polymers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 4207
Author(s):  
Krissia Wilhelm Romero ◽  
María Isabel Quirós ◽  
Felipe Vargas Huertas ◽  
José Roberto Vega-Baudrit ◽  
Mirtha Navarro-Hoyos ◽  
...  

Polymeric lipid hybrid nanoparticles (PLHNs) are the new generation of drug delivery systems that has emerged as a combination of a polymeric core and lipid shell. We designed and optimized a simple method for the preparation of Pluronic F-127-based PLHNs able to load separately demethoxycurcumin (DMC) and bisdemethoycurcumin (BDM). CUR was used as a model compound due to its greater availability from turmeric and its structure similarity with DMC and BDM. The developed method produced DMC and BDM-loaded PLHNs with a size average of 75.55 ± 0.51 and 15.13 ± 0.014 nm for DMC and BDM, respectively. An FT-IR analysis confirmed the encapsulation and TEM images showed their spherical shape. Both formulations achieved an encapsulation efficiency ≥ 92% and an exhibited significantly increased release from the PLHN compared with free compounds in water. The antioxidant activity was enhanced as well, in agreement with the improvement in water dissolution; obtaining IC50 values of 12.74 ± 0.09 and 16.03 ± 0.55 for DMC and BDM-loaded PLHNs, respectively, while free curcuminoids exhibited considerably lower antioxidant values in an aqueous solution. Hence, the optimized PHLN synthesis method using CUR as a model and then successfully applied to obtain DMC and BDM-loaded PLHNs can be extended to curcuminoids and molecules with a similar backbone structure to improve their bioactivities.


2021 ◽  
Vol 11 (3) ◽  
pp. 1-13
Author(s):  
Andrzej Matczak ◽  
Przemysław A. Pawlicki

The aim of this study is to characterize the tourism activity of Polish cannabis consumers in terms of (i) the level of their participation in tourism, (ii) parameters describing this participation, (iii) the effect of legal access to cannabis on choosing tourism destinations. The study is based on an anonymous online survey in which 886 voluntary respondents answered a series of questions about their tourist travels, their attitude to cannabis consumption, and their demographic, socio-economic and geographic metrics. Results of the survey were analyzed using several statistical indicators of variability, structure, correlation, and structure similarity. For the respondents declaring cannabis consumption, the level of their participation in tourism is close to the national level. Other parameters describing the domestic and foreign tourism of these respondents differ quite significantly from those reported for the general public of Poland. This indicates that the possibility of cannabis consumption significantly affects the nature and directions of travels undertaken by tourists interested in cannabis. Furthermore, there is a strong connection between the respondents’ personal preferences and the nature of their tourism, especially the destinations of their foreign trips. The conclusions from this study mostly apply to current and recent cannabis consumers because the vast majority of respondents (90%) rank among such kinds of cannabis users.


2021 ◽  
Author(s):  
Maarten L Hekkelman ◽  
Ida de de Vries ◽  
Robbie P Joosten ◽  
Anastassis Perrakis

Artificial intelligence (AI) methods for constructing structural models of proteins on the basis of their sequence are having a transformative effect in biomolecular sciences. The AlphaFold protein structure database makes available hundreds of thousands of protein structures. However, all these structures lack cofactors essential for their structural integrity and molecular function (e.g. hemoglobin lacks a bound heme), key ions essential for structural integrity (e.g. zinc-finger motifs) or catalysis (e.g. Ca2+ or Zn2+ in metalloproteases), and ligands that are important for biological function (e.g. kinase structures lack ADP or ATP). Here, we present AlphaFill, an algorithm based on sequence and structure similarity, to "transplant" such "missing" small molecules and ions from experimentally determined structures to predicted protein models. These publicly available structural annotations are mapped to predicted protein models, to help scientists interpret biological function and design experiments.


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