BACKGROUND: Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. RESULTS: This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. CONCLUSIONS: Traveler is a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout. It is available at http://github.com/davidhoksza/traveler .

• Klíčová slova
• RNA secondary structure, Software tool, Template-based modeling, Visualization,
• MeSH
• algoritmy MeSH
• konformace nukleové kyseliny MeSH
• RNA chemie   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RNA MeSH

INTRODUCTION: T-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. While a large number of TCR sequences specific to different antigenic peptides are known to date, the structural data describing the conformation and contacting residues for TCR-peptide-MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of these complexes using TCR sequences with known specificity. METHODS: Identification of CDR3 sequences and their further clustering, based on available spatial structures, V- and J-genes of corresponding T-cell receptors, and epitopes, was performed using the VDJdb database. Modeling of the selected CDR3 loops was conducted using a stepwise introduction of single amino acid substitutions to the template PDB structures, followed by optimization of the TCR-peptide-MHC contacting interface using the Rosetta package applications. Statistical analysis and recursive feature elimination procedures were carried out on computed energy values and properties of contacting amino acid residues between CDR3 loops and peptides, using R. RESULTS: Using the set of 29 complex templates (including a template with SARS-CoV-2 antigen) and 732 specificity records, we built a database of 1585 model structures carrying substitutions in either TCRα or TCRβ chains with some models representing the result of different mutation pathways for the same final structure. This database allowed us to analyze features of amino acid contacts in TCR - peptide interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues. CONCLUSION: Our results provide a methodology for creating high-quality TCR-peptide-MHC models for antigens of interest that can be utilized to predict TCR specificity.

• Klíčová slova
• T-cell receptor, TCR-peptide-MHC complex, antigen recognition, database, structural modeling,
• MeSH
• aminokyseliny MeSH
• antigenní specifita receptorů T-buněk MeSH
• COVID-19 * MeSH
• komplement MeSH
• lidé MeSH
• SARS-CoV-2 MeSH
• specificita protilátek MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• komplement MeSH

Pharmacophore modeling is a widely used strategy for finding new hit molecules. Since not all protein targets have available 3D structures, ligand-based approaches are still useful. Currently, there are just a few free ligand-based pharmacophore modeling tools, and these have a lot of restrictions, e.g., using a template molecule for alignment. We developed a new approach to 3D pharmacophore representation and matching which does not require pharmacophore alignment. This representation can be used to quickly find identical pharmacophores in a given set. Based on this representation, a 3D pharmacophore ligand-based modeling approach to search for pharmacophores which preferably match active compounds and do not match inactive ones was developed. The approach searches for 3D pharmacophore models starting from 2D structures of available active and inactive compounds. The implemented approach was successfully applied for several retrospective studies. The results were compared to a 2D similarity search, demonstrating some of the advantages of the developed 3D pharmacophore models. Also, the generated 3D pharmacophore models were able to match the 3D poses of known ligands from their protein-ligand complexes, confirming the validity of the models. The developed approach is available as an open-source software tool: http://www.qsar4u.com/pages/pmapper.php and https://github.com/meddwl/psearch.

• Klíčová slova
• 3D pharmacophore hash, 3D pharmacophore signatures, ligand-based modeling, pharmacophore modeling,
• MeSH
• antagonisté adenosinového receptoru A2 chemie   MeSH
• cholinesterasové inhibitory chemie   MeSH
• inhibitory cytochromu P450 CYP3A chemie   MeSH
• ligandy MeSH
• molekulární modely * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antagonisté adenosinového receptoru A2 MeSH
• cholinesterasové inhibitory MeSH
• inhibitory cytochromu P450 CYP3A MeSH
• ligandy MeSH

The human dopamine, norepinephrine, and serotonin transporters (hDAT, hNET, and hSERT) are carriers of neurotransmitters and targets for many drugs. Pioneering works in the past three years to elucidate experimental models of the Drosophila dDAT and human hSERT structures will rapidly impact the field of neuroscience. Here, we evaluated automated homology-based human models of these transporters, employing systematic physics-based, knowledge-based, and empirical-based check. Modeling guidelines were conveyed with attention to the central binding site (S1), secondary binding site (S2), and the extracellular loops EL2 and EL4. Application of new experimental models (dDAT and hSERT) will improve the accuracy of homology models, previously utilizing prokaryotic leucine transporter (LeuT) structure, and provide better predictions of ligand interactions, which is required for understanding of cellular mechanisms and for development of novel therapeutics.

• Klíčová slova
• Homology-based, dopamine transporter, norepinephrine transporter, protein structure, serotonin transporter, template-based,
• MeSH
• acetyltransferasy genetika   metabolismus   MeSH
• Drosophila MeSH
• konformace proteinů MeSH
• lidé MeSH
• membránové transportní proteiny pro serotonin genetika   metabolismus   MeSH
• molekulární modely * MeSH
• proteiny Drosophily genetika   metabolismus   MeSH
• proteiny přenášející dopamin přes plazmatickou membránu genetika   metabolismus   MeSH
• proteiny přenášející noradrenalin přes plazmatickou membránu genetika   metabolismus   MeSH
• rozpoznávání automatizované MeSH
• sekvenční homologie aminokyselin * MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• Názvy látek
• AANAT1 protein, Drosophila MeSH Prohlížeč
• acetyltransferasy MeSH
• membránové transportní proteiny pro serotonin MeSH
• proteiny Drosophily MeSH
• proteiny přenášející dopamin přes plazmatickou membránu MeSH
• proteiny přenášející noradrenalin přes plazmatickou membránu MeSH
• SLC6A2 protein, human MeSH Prohlížeč
• SLC6A4 protein, human MeSH Prohlížeč

To employ dual advantages of emulsion and gel, a facile approach was investigated to fabricate core/shells structured hydrogel beads based on sodium alginate (SA) via Pickering emulsion template and in situ gelation. The encapsulation and controlled release behavior were further studied using lysozyme (Ly) as the model protein. The optical micrographs and SEM images indicated the SA beads could well disperse with the size about 150 μm. CaCO3 microparticles were strong adhesive onto SA gel. It showed that 96.51 ± 0.62% Ly was loaded into the hydrogel beads. The released behavior of Ly could be regulated by external pH condition, and displayed highest release rate at pH 5.0. Whereas the lowest release rate was recorded at pH 7.0. The released behavior well followed the Hixcon-Crowell model which indicated that the release mechanism of Ly followed the corrosion diffusion law. The worth-while endeavor provide an artful and facile approach using Pickering emulsion template and in situ gelation to fabricate core/shells structured SA beads with high load capacity and controlled regulation of the entrapped functional component.

• Klíčová slova
• Calcium carbonate, Controlled release, Gel, Lysozyme, Sodium alginate,
• MeSH
• algináty chemie   MeSH
• difuze MeSH
• emulze MeSH
• hydrogely chemie   MeSH
• kinetika MeSH
• koncentrace vodíkových iontů MeSH
• léky s prodlouženým účinkem * MeSH
• muramidasa chemie   MeSH
• příprava léků metody   MeSH
• roztoky MeSH
• uhličitan vápenatý chemie   MeSH
• uvolňování léčiv MeSH
• změna skupenství MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• algináty MeSH
• emulze MeSH
• hydrogely MeSH
• léky s prodlouženým účinkem * MeSH
• muramidasa MeSH
• roztoky MeSH
• uhličitan vápenatý MeSH

Targeted therapy is a promising approach for treatment of neuroblastoma as evident from the large number of targeting agents employed in clinical practice today. In the absence of known crystal structures, researchers rely on homology modeling to construct template-based theoretical structures for drug design and testing. Here, we discuss three candidate cell surface proteins that are suitable for homology modeling: human norepinephrine transporter (hNET), anaplastic lymphoma kinase (ALK), and neurotrophic tyrosine kinase receptor 2 (NTRK2 or TrkB). When choosing templates, both sequence identity and structure quality are important for homology modeling and pose the first of many challenges in the modeling process. Homology modeling of hNET can be improved using template models of dopamine and serotonin transporters instead of the leucine transporter (LeuT). The extracellular domains of ALK and TrkB are yet to be exploited by homology modeling. There are several idiosyncrasies that require direct attention throughout the process of model construction, evaluation and refinement. Shifts/gaps in the alignment between the template and target, backbone outliers and side-chain rotamer outliers are among the main sources of physical errors in the structures. Low-conserved regions can be refined with loop modeling method. Residue hydrophobicity, accessibility to bound metals or glycosylation can aid in model refinement. We recommend resolving these idiosyncrasies as part of "good modeling practice" to obtain highest quality model. Decreasing physical errors in protein structures plays major role in the development of targeting agents and understanding of chemical interactions at the molecular level.

• Klíčová slova
• anaplastic lymphoma kinase, homology modeling, neuroblastoma, neurotrophic tyrosine kinase receptor, norepinephrine transporter, targeted therapy,
• Publikační typ
• časopisecké články MeSH

Twelve homology models of the human M2 muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M3 muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.

• MeSH
• konformace proteinů * MeSH
• krystalografie rentgenová * MeSH
• lidé MeSH
• molekulární modely MeSH
• receptor muskarinový M2 chemie   MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin MeSH
• simulace molekulového dockingu MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• CHRM2 protein, human MeSH Prohlížeč
• receptor muskarinový M2 MeSH

Computed tomography (CT) is an effective diagnostic modality for three-dimensional imaging of bone structures, including the geometry of their defects. The aim of the study was to create and optimize 3D geometrical and real plastic models of the distal femoral component of the knee with joint surface defects. Input data included CT images of stifle joints in twenty miniature pigs with iatrogenic osteochondrosis-like lesions in medial femoral condyle of the left knee. The animals were examined eight and sixteen weeks after surgery. Philips MX 8000 MX and View workstation were used for scanning parallel plane cross section slices and Cartesian discrete volume creation. On the average, 100 slices were performed in each stifle joint. Slice matrices size was 512 x 512 with slice thickness of 1 mm. Pixel (voxel) size in the slice plane was 0.5 mm (with average accuracy of +/-0.5 mm and typical volume size 512 x 512 x 100 voxels). Three-dimensional processing of CT data and 3D geometrical modelling, using interactive computer graphic system MediTools formerly developed here, consisted of tissue segmentation (raster based method combination and 5 % of manual correction), vectorization by the marching-cubes method, smoothing and decimation. Stifle- joint CT images of three individuals of different body size (small, medium and large) were selected to make the real plastic models of their distal femurs from plaster composite using rapid prototyping technology of Zcorporation. Accuracy of the modeling was +/- 0.5 mm. The real plastic models of distal femurs can be used as a template for developing custom made press and fit scaffold implants seeded with mesenchymal stem cells that might be subsequently implanted into iatrogenic joint surface defects for articular cartilage-repair enhancement.

• MeSH
• anatomické modely * MeSH
• design s pomocí počítače MeSH
• femur diagnostické zobrazování   MeSH
• kolenní kloub u koně, psa diagnostické zobrazování   MeSH
• kultivované buňky MeSH
• mezenchymální kmenové buňky * MeSH
• miniaturní prasata MeSH
• modely nemocí na zvířatech MeSH
• osteochondritida diagnostické zobrazování   MeSH
• počítačová rentgenová tomografie * MeSH
• prasata MeSH
• protézy - design MeSH
• rentgenový obraz - interpretace počítačová MeSH
• tkáňové inženýrství * MeSH
• tkáňové podpůrné struktury * MeSH
• zobrazování trojrozměrné * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

OBJECTIVES: To compare traditional plaster casts, digital models and 3D printed copies of dental plaster casts based on various criteria. To determine whether 3D printed copies obtained using open source system RepRap can replace traditional plaster casts in dental practice. To compare and contrast the qualities of two possible 3D printing options--source system RepRap and commercially available 3D printing. DESIGN AND SETTINGS: A method comparison study on 10 dental plaster casts from the Orthodontic department, Department of Stomatology, 2nd medical Faulty, Charles University Prague, Czech Republic. MATERIAL AND METHODS: Each of 10 plaster casts were scanned by inEos Blue scanner and the printed on 3D printer RepRap [10 models] and ProJet HD3000 3D printer [1 model]. Linear measurements between selected points on the dental arches of upper and lower jaws on plaster casts and its 3D copy were recorded and statistically analyzed. RESULTS: 3D printed copies have many advantages over traditional plaster casts. The precision and accuracy of the RepRap 3D printed copies of plaster casts were confirmed based on the statistical analysis. Although the commercially available 3D printing enables to print more details than the RepRap system, it is expensive and for the purpose of clinical use can be replaced by the cheaper prints obtained from RepRap printed copies. CONCLUSIONS: Scanning of the traditional plaster casts to obtain a digital model offers a pragmatic approach. The scans can subsequently be used as a template to print the plaster casts as required. Using 3D printers can replace traditional plaster casts primarily due to their accuracy and price.

• MeSH
• anatomické modely * MeSH
• sádrové obvazy * MeSH
• tiskařství přístrojové vybavení   MeSH
• zubní lékařství * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Parcellation-based approaches are an important part of functional magnetic resonance imaging data analysis. They are a necessary processing step for sorting data in structurally or functionally homogenous regions. Real functional magnetic resonance imaging datasets usually do not cover the atlas template completely; they are often spatially constrained due to the physical limitations of MR sequence settings, the inter-individual variability in brain shape, etc. When using a parcellation template, many regions are not completely covered by actual data. This paper addresses the issue of the area coverage required in real data in order to reliably estimate the representative signal and the influence of this kind of data loss on network analysis metrics. We demonstrate this issue on four datasets using four different widely used parcellation templates. We used two erosion approaches to simulate data loss on the whole-brain level and the ROI-specific level. Our results show that changes in ROI coverage have a systematic influence on network measures. Based on the results of our analysis, we recommend controlling the ROI coverage and retaining at least 60% of the area in order to ensure at least 80% of explained variance of the original signal.

• Klíčová slova
• Atlas, Coverage, Parcellation, Representative signal, fMRI,
• MeSH
• algoritmy MeSH
• atlasy jako téma * MeSH
• dospělí MeSH
• funkční lateralita MeSH
• individualita MeSH
• lidé MeSH
• lineární modely MeSH
• magnetická rezonanční tomografie metody   statistika a číselné údaje   MeSH
• mapování mozku metody   MeSH
• mladý dospělý MeSH
• mozek diagnostické zobrazování   MeSH
• počítačová simulace MeSH
• počítačové zpracování obrazu metody   MeSH
• reprodukovatelnost výsledků MeSH
• světelná stimulace MeSH
• zdraví dobrovolníci pro lékařské studie MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH