The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.

• MeSH
• algoritmy MeSH
• aminokyseliny chemie   MeSH
• biologické modely MeSH
• databáze proteinů MeSH
• internet MeSH
• ionty MeSH
• koncentrace vodíkových iontů MeSH
• ligandy MeSH
• počítačová simulace MeSH
• posttranslační úpravy proteinů MeSH
• proteiny chemie   MeSH
• rozpouštědla MeSH
• sbalování proteinů MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• software MeSH
• strojové učení MeSH
• strukturní homologie proteinů MeSH
• voda MeSH
• výpočetní biologie metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• ionty MeSH
• ligandy MeSH
• proteiny MeSH
• rozpouštědla MeSH
• voda MeSH

BACKGROUND: Attention is focused on the health and physical fitness of older adults due to their increasing age. Maintaining physical abilities, including safe walking and movement, significantly contributes to the perception of health in old age. One of the early signs of declining fitness in older adults is limited mobility. Approximately one third of 70-year-olds and most 80-year-olds report restrictions on mobility in their apartments and immediate surroundings. Restriction or loss of mobility is a complex multifactorial process, which makes older adults prone to falls, injuries, and hospitalizations and worsens their quality of life while increasing overall mortality. OBJECTIVE: The objective of the study is to identify the factors that have had a significant impact on mobility in recent years and currently, and to identify gaps in our understanding of these factors. The study aims to highlight areas where further research is needed and where new and effective solutions are required. METHODS: The PRISMA methodology was used to conduct a scoping review in the Scopus and Web of Science databases. Papers published from 2007 to 2021 were searched in November 2021. Of these, 52 papers were selected from the initial 788 outputs for the final analysis. RESULTS: The final selected papers were analyzed, and the key determinants were found to be environmental, physical, cognitive, and psychosocial, which confirms the findings of previous studies. One new determinant is technological. New and effective solutions lie in understanding the interactions between different determinants of mobility, addressing environmental factors, and exploring opportunities in the context of emerging technologies, such as the integration of smart home technologies, design of accessible and age-friendly public spaces, development of policies and regulations, and exploration of innovative financing models to support the integration of assistive technologies into the lives of seniors. CONCLUSION: For an effective and comprehensive solution to support senior mobility, the determinants cannot be solved separately. Physical, cognitive, psychosocial, and technological determinants can often be perceived as the cause/motivation for mobility. Further research on these determinants can help to arrive at solutions for environmental determinants, which, in turn, will help improve mobility. Future studies should investigate financial aspects, especially since many technological solutions are expensive and not commonly available, which limits their use.

• Klíčová slova
• Determinants, Financial aspects, Mobility, Older adults, Technological solutions,
• MeSH
• chůze * MeSH
• cvičení MeSH
• databáze faktografické MeSH
• kvalita života * MeSH
• lidé MeSH
• senioři MeSH
• tělesná výkonnost MeSH
• Check Tag
• lidé MeSH
• senioři MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.

• Klíčová slova
• digital twin, electron microscopy, multislice simulation, tomography,
• MeSH
• databáze proteinů MeSH
• počítačová simulace MeSH
• počítačové zpracování obrazu metody   MeSH
• proteiny ultrastruktura   MeSH
• software MeSH
• tomografie elektronová přístrojové vybavení   metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny MeSH

Vehicle-tree collisions are the most common type of road crash with fixed obstacle in Czech Republic. Based on the literature review and using real world in-depth crash data, this paper aims to define factors, which significantly influence the injury severity of single vehicle-tree crashes. In-depth data provide a comprehensive view to the failure on the system infrastructure-human-vehicle related to crash, the in-depth crash database include very detailed information related to infrastructure, vehicle, human failure and crash participants characteristics and their medical condition and also crash reconstruction. Multinomial logistic regression and generalized linear mixed model were used to determine the individual effect of each predictor. The statistically significant variables were the day period, trunk diameter and impact speed. Using multinomial logistic regression shows also vehicle age as statistically significant. Obtained results can help to efficiently direct countermeasures not only on the road infrastructure-e.g. speed reduction in selected locations with specified tree character. However, the emphasis should be also focused on driver behaviour.

• MeSH
• databáze faktografické MeSH
• dopravní nehody * MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• lineární modely MeSH
• logistické modely MeSH
• mladiství MeSH
• mladý dospělý MeSH
• rány a poranění etiologie   patologie   MeSH
• rizikové faktory MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• stromy MeSH
• stupeň závažnosti nemoci MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

• Klíčová slova
• PDB, Protein Data Bank, ligands, three-dimensional macromolecular structure, validation,
• MeSH
• databáze proteinů * MeSH
• konformace proteinů * MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• ligandy MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• proteiny analýza   chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH
• Názvy látek
• ligandy MeSH
• makromolekulární látky MeSH
• proteiny MeSH

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

• MeSH
• databáze proteinů * MeSH
• datové kurátorství MeSH
• konformace proteinů MeSH
• krystalografie rentgenová MeSH
• ligandy MeSH
• molekulární modely MeSH
• proteiny chemie   MeSH
• směrnice jako téma MeSH
• Publikační typ
• kongresy MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• ligandy MeSH
• proteiny MeSH

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.

• MeSH
• databáze proteinů * MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• peptidy izolace a purifikace   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• srovnávací studie MeSH
• Názvy látek
• peptidy MeSH

A new database of nucleic acid base trimers has been developed that includes 141 geometries and stabilization energies obtained at the RI-MP2 level of theory with the TZVPP basis set. Compared to previously compiled biologically oriented databases, this new construct includes considerably more complicated structures; the various intermolecular interactions in the trimers are quite heterogeneous and in particular include simultaneous hydrogen bonding and stacking interactions, which is similar to the situation in actual biopolymers. Validation against these benchmark data is therefore a more demanding task for approximate models, since correct descriptions of all energy terms are unlikely to be accomplished by fortuitous cancellations of systematic errors. The density functionals TPSS (both with and without an empirical dispersion term), PWB6K, M05-2X, and BH&H, and the self-consistent charge density functional tight binding method augmented with an empirical dispersion term (SCC-DFTB-D) were assessed for their abilities accurately to compute structures and energies. The best reproduction of the BSSE corrected RI-MP2 stabilization energies was achieved by the TPSS functional (TZVPP basis set) combined with empirical dispersion; removal of the dispersion correction leads to significantly degraded performance. The M05-2X and PWB6K functionals performed very well in reproducing the RI-MP2 geometries, but showed a systematic moderate underestimation of the magnitude of base stacking interactions. The SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2; given its computational efficiency it represents a good option for initial scanning of analogous biopolymeric potential energy surfaces. BH&H gives geometries of comparable quality to the other functionals but significantly overestimates interaction energies other than stacking.

• MeSH
• databáze nukleových kyselin * MeSH
• konformace nukleové kyseliny * MeSH
• oligonukleotidy chemie   MeSH
• termodynamika * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• oligonukleotidy MeSH

Four accessions of hexaploid Elymus repens from its native Central European distribution area were analyzed using sequencing of multicopy (internal transcribed spacer, ITS) and single-copy (granule-bound starch synthase I, GBSSI) DNA in concert with genomic and fluorescent in situ hybridization (GISH and FISH) to disentangle its allopolyploid origin. Despite extensive ITS homogenization, nrDNA in E. repens allowed us to identify at least four distinct lineages. Apart from Pseudoroegneria and Hordeum, representing the major genome constituents, the presence of further unexpected alien genetic material, originating from species outside the Triticeae and close to Panicum (Paniceae) and Bromus (Bromeae), was revealed. GBSSI sequences provided information complementary to the ITS. Apart from Pseudoroegneria and Hordeum, two additional gene variants from within the Triticeae were discovered: One was Taeniatherum-like, but the other did not have a close relationship with any of the diploids sampled. GISH results were largely congruent with the sequence-based markers. GISH clearly confirmed Pseudoroegneria and Hordeum as major genome constituents and further showed the presence of a small chromosome segment corresponding to Panicum. It resided in the Hordeum subgenome and probably represents an old acquisition of a Hordeum progenitor. Spotty hybridization signals across all chromosomes after GISH with Taeniatherum and Bromus probes suggested that gene acquisition from these species is more likely due to common ancestry of the grasses or early introgression than to recent hybridization or allopolyploid origin of E. repens. Physical mapping of rDNA loci using FISH revealed that all rDNA loci except one minor were located on Pseudoroegneria-derived chromosomes, which suggests the loss of all Hordeum-derived loci but one. Because homogenization mechanisms seem to operate effectively among Pseudoroegneria-like copies in this species, incomplete ITS homogenization in our samples is probably due to an interstitial position of an individual minor rDNA locus located within the Hordeum-derived subgenome.

• MeSH
• Bayesova věta MeSH
• cytogenetické vyšetření metody   MeSH
• databáze genetické MeSH
• fylogeneze MeSH
• genetická transkripce MeSH
• hybridizace in situ fluorescenční MeSH
• intergenová DNA MeSH
• lipnicovité genetika   MeSH
• modely genetické * MeSH
• přenos genů horizontální MeSH
• pseudogeny MeSH
• ribozomální DNA MeSH
• rostlinné geny * MeSH
• synthasa škrobu genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• granule-bound starch synthase I MeSH Prohlížeč
• intergenová DNA MeSH
• ribozomální DNA MeSH
• synthasa škrobu MeSH

OBJECTIVES: To determine modifiable factors related to abusive behaviors in nursing home residents with dementia. DESIGN: Analysis of Minimum Data Set (MDS) of the Resident Assessment Instrument (RAI) information. SETTING: We used MDS-RAI data from 8 Dutch nursing homes and 10 residential homes that volunteered to collect data for care planning. We included the data of residents within a 12-month time window for each facility separately, resulting in a range from April 4, 2007, to December 1, 2008. PARTICIPANTS: We selected 929 residents older than 65 with Alzheimer's disease or other dementia who were dependent in decision making and not comatose. MEASUREMENTS: Cognitive Performance Scale, MDS Depression Scale and several individual items from the MDS-RAI (ability to understand others, verbally and physically abusive behavioral symptoms, resist care, diagnosis of Alzheimer's disease and of dementia other than Alzheimer's disease, diagnosis of depression, presence of delusions, hallucinations, pain frequency and constipation, and number of days receiving medications). RESULTS: Resistiveness to care, related to lack of understanding, depression, hallucinations and delusions, was strongly related to abusive behaviors. Presence of depressive symptoms and delusions was also related to abusive behaviors independent of resistiveness to care. Only very few residents who understood others and were not depressed were abusive. CONCLUSION: Abusive behaviors may develop from lack of understanding leading to resistiveness to care. Behavioral interventions preventing escalation of resistiveness to care into combative behavior and the treatment of depression can be expected to decrease or prevent abusive behavior of most nursing home residents with dementia.

• MeSH
• agrese psychologie   MeSH
• Alzheimerova nemoc komplikace   psychologie   MeSH
• databáze faktografické MeSH
• demence komplikace   psychologie   terapie   MeSH
• domovy pro seniory * MeSH
• incidence MeSH
• kognitivní poruchy komplikace   psychologie   terapie   MeSH
• kohortové studie MeSH
• lidé MeSH
• logistické modely MeSH
• multivariační analýza MeSH
• odmítnutí terapie pacientem MeSH
• pečovatelské domovy * MeSH
• pravděpodobnost MeSH
• psychiatrické posuzovací škály MeSH
• psychomotorický neklid epidemiologie   etiologie   MeSH
• rizikové faktory MeSH
• rozložení podle pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• stupeň závažnosti nemoci MeSH
• věkové rozložení MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH