TMFoldWeb: a web server for predicting transmembrane protein fold class.

BACKGROUND: Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. RESULTS: An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. CONCLUSIONS: The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices. REVIEWERS: This article was reviewed by Dr. Michael Gromiha, Dr. Sandor Pongor and Dr. Frank Eisenhaber with Wing-Cheong Wong

Supporting Digital Supply Chains by IoT Frameworks: Collaboration, Control, Combination

The purpose of this paper is to introduce a technology-oriented SCM (Supply Chain Management) development methodology, which can be used in the design of IoT (Internet of Things) frameworks especially characterized by supply chain processes. In order to meet DSC (Digital Supply Chain) expectations, two areas are examined in detail during the literature review. Firstly, the current SCM models are studied. Secondly, Industry 4.0 requirements had to be surveyed. As a consequence, challenges and gaps are identified for which we seek the solution during our research. Based on the results, it can be stated that digitization has definitely required an improved technological solution that IoT frameworks can provide. The result is a technology-driven, IoT-based SCM development methodology that serves as a basis for the design of such platforms, which will manage supply chains. To prove the feasibility of the proposed development methodology, the Arrowhead industrial IoT framework is used for validation

EXAMINATION OF AMBULANCE ARRIVAL TIMES BY GEOINFORMATICS TOOLS – EXAMPLE OF BORSOD-ABAÚJZEMPLÉN COUNTY (HUNGARY)

An essential part of the health system is the ambulance service, whose main task is to provide patients with high quality care. In the spirit of the above, the aim of the study is to explore the spatial characteristics of the ambulance service in a Hungarian territorial unit, Borsod-Abaúj-Zemplén county. The main findings of the study are: - The geographical location of ambulance stations in the county is strongly influenced by geography and demographic characteristics. - The designation of the coverage areas of ambulance station is fundamentally consistent with the access time to the respective ambulance stations. - The accessibility of each settlement from the ambulance station and the time needed to travel the ambulance station - location - hospital route differ for the speed allowed by the Highway Code and for the speed of 60 km/h

The formation kinetic of mechanochemical synthesized perovskites

In this study, we aimed to achieve mechanochemical perovskite synthesis and to quantify the energy used during milling (Eb - impact energy and Ecum - cumulative energy) and to describe the relationship between them. For mechanochemical treatment a Fritsch Pulverisette-6 type planetary ball mill was used. As a model compound the widely used barium-titanate (BaTiO3) was chosen, which was produced by the reaction of barium-oxide (BaO) and titanate-dioxide (TiO2). The aim was to track the formation of BaTiO3 and to determine the minimum milling energies required for its production. Three important parameters were considered for the calculation of energy values: the material of the milling vials and balls, the number of balls and the speed of rotation. The transformation was tracked by X-ray diffraction (XRD) measurement, and the applied energy was determined using the Burgio-Rojac energy model. Our goal was to draw conclusions that can be used to predetermine optimal milling parameters in the production of other perovskite structured materials. The hypothesis was verified by the mechanochemical synthesis of zinc-titanate (ZnTiO3) which was produced by the reaction of zinc-oxide (ZnO) and TiO2

Transzmembán fehérjék elméleti szerkezet vizsgálata és tudásbázisa = Knowledge base and theoretical structure analysis of transmembrane proteins

A projekt során elkészítettük a TOPDB adatbázis új web interfészét meghajtó programkönyvtárat (Xbuilder), továbbá módosítottuk a HMMTOP transzmembrán topológia becslő algoritmust oly módon, hogy a meghatározott topológiai kísérleti adatokat, még ha azok ellentmondóak is, figyelembe tudja venni a topológia becslés során. A HMMTOP algoritmusról, annak helyes használatáról, valamint a módosításokról az ebben az időben készült, felkérésre írt könyvfejezetben részletesen is írtunk, valamint a módosított algoritmust – egy amerikai csoporttal együttműködésben - sikeresen alkalmaztuk egy eddig még ismeretlen topológiájú fehérje, a SLC20A1 jelű foszfát transzporter fehérje topológia becsléséhez. Az erről készült munkánk a J. Biol. Chem. folyóiratban publikáltuk. A transzmembrán fehérjék membránban való pontos helyzetének a meghatározásához szükséges új eljárás kidolgozása az APBS eljárás felhasználásával számos problémába ütköztünk és míg ezeken dolgoztunk Callenberg és mtsai közöltek egy cikket, amelyben az általunk felvetett és megoldani kívánt problémát nagyon részletesen leírták, és megoldották. A transzmembán fehérjék szerkezetvizsgálatához kidolgoztunk egy eljárást, amely az XBuilder programcsomagot használva lehetővé teszi a fehérjékben levő atomi kontaktus vizsgálatát, illetve a különböző kontaktus becslő módszerek eredményeinek a tesztelését. Ez a munkánk a Nucleic Acids Research 2012-es adatbázis különszámában jelenik meg. | We have developed the XBuilder program library which is planned to be the engine of the new TOPDB web interface. We have modified the HMMTOP algorithm in a way that it can incorporate the results of various experiments as constraints during the prediction. We were invited to write a review, where the main aspects and usage of HMMTOP algorithm together with these modifications have been discussed. Using this modified version of HMMTOP – cooperating with a group from the NIH - we have successfully predicted and established the topology of the SLC20A1 phosphate transporter. This work has been published in the J. Biol. Chem. During the course of developing a new algorithm to determine the membrane localization of transmembrane proteins by the APBS methods, we have faced to several problems, and while we try to solve them, Callenberg etal come in a solution to these problems. For investigating the structure and atomic contacts in transmembrane proteins we have developed a new web interface, called CMWeb, which utilize the XBuilder program library. This web interface can be used for analyzing and visualizing residue-residue contacts in proteins as well as to benchmark test the results of various contact prediction methods. This work is published in the 2012 NAR Database issue

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

The PDBTM database (available at http://pdbtm .enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ~400 to 1700 entries but also new structural elements have been identified, in addition to the well-known a-helical bundle and b-barrel structures. Numerous ‘exotic’ transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community