The IntAct database: efficient access to fine-grained molecular interaction data.
Ontology highlight
ABSTRACT:
SUBMITTER: Del Toro N
PROVIDER: S-EPMC8728211 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains approximately 2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.
| S-EPMC308786 | biostudies-literature
Project description:In the medical system, the verification, preservation and synchronization of electronic medical records has always been a difficult problem, and the random dissemination of patient records will bring various risks to patient privacy. Therefore, how to achieve secure data sharing on the basis of ensuring users' personal privacy becomes the key. In recent years, blockchain has been proposed to be a promising solution to achieve data sharing with security and privacy preservation due to its advantages of immutability. So, a distributed electronic medical records searchable scheme was proposed by leveraging blockchain and smart contract technology. Firstly, we perform a hash calculation on the electronic medical data and store the corresponding value on the blockchain to ensure its integrity and authenticity. Then, we encrypt the electronic medical data and store it in the interplanetary file system which is a distributed storage protocol. These operations not only can solve centralized data store of servers of several medical institutions, but also be good at lowering stress from data store and high-frequency access to blockchain. Secondly, the encrypted keyword index information of electronic medical records was stored on the Ethereum blockchain, meanwhile a smart contract deployed in the Ethereum blockchain is used to realize keyword search instead of depending on a centralized third party. Furthermore, we use attribute-based encryption scheme to ensure that only the attributes meeting the access policy can decrypt the encrypted electronic medical records. Finally, our performance analysis and security analysis show that the scheme is secure and efficient.
| S-EPMC7537906 | biostudies-literature
Project description:In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone phi,psi angles with the first side-chain torsion angles (chi(1)) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found that residue volumes exhibit dependency on backbone 2 degrees structure conformation: side-chains pack more densely in extended beta-sheet than in alpha-helical structures. As expected, residue volumes on the protein surface were larger than those in the interior. The first side-chain torsion angles are found to be dependent on the backbone conformations in agreement with previous studies, but the dynameome dataset provides higher resolution of rotamer preferences based on the backbone conformation. All three gauche(-), gauche(+), and trans rotamers show different patterns of phi,psi dependency, and variations in chi(1) value are skewed from their canonical values to relieve the steric strains. By demonstrating the utility of dynameomic modeling on the native state ensemble, this study reveals details of the interplay among backbone conformations, residue volumes and side-chain conformations.
| S-EPMC2916028 | biostudies-literature
Project description:Fog computing can extend cloud computing to the edge of the network so as to reduce latency and network congestion. However, existing encryption schemes were rarely used in fog environment, resulting in high computational and storage overhead. Aiming at the demands of local information for terminal device and the shortcomings of cloud computing framework in supporting mobile applications, by taking the hospital scene as an example, a searchable personal health records framework with fine-grained access control in cloud-fog computing is proposed. The proposed framework combines the attribute-based encryption (ABE) technology and search encryption (SE) technology to implement keyword search function and fine-grained access control ability. When keyword index and trapdoor match are successful, the cloud server provider only returns relevant search results to the user, thus achieving a more accurate search. At the same time, the scheme is multi-authority, and the key leakage problem is solved by dividing the user secret key distribution task. Moreover, in the proposed scheme, we securely outsource part of the encryption and decryption operations to the fog node. It is effective both in local resources and in resource-constrained mobile devices. Based on the decisional q-parallel bilinear Diffie-Hellman exponent (q-DBDHE) assumption and decisional bilinear Diffie-Hellman (DBDH) assumption, our scheme is proven to be secure. Simulation experiments show that our scheme is efficient in the cloud-fog environment.
| S-EPMC6264141 | biostudies-literature
Project description:The study of drug-target interaction plays an important role in the process of drug development. The subject of DTI forecasting has advanced significantly in the last several years, yielding numerous significant research findings and methodologies. Heterogeneous data sources provide richer information and comprehensive perspectives for drug-target interaction prediction, so many existing methods rely on heterogeneous networks, and graph embedding technology becomes an important technology to extract information from heterogeneous networks. These approaches, however, are less concerned with potential noisy information in heterogeneous networks and more focused on the extent of information extraction in those networks. Based on this, a potential DTI predictive network model called FBRWPC is proposed in this paper. It uses a fine-grained similarity selection program to first integrate similarity on similar networks and then a bidirectional random walk graph embedding learning method with restart to obtain an updated drug target interaction matrix. Through the use of similarity selection and fine-grained selection similarity integration, the framework can effectively filter out the noise present in heterogeneous networks and enhance the model's prediction performance. The experimental findings demonstrate that, even after being split up into four distinct types of data sets, FBRWPC can still retain great prediction performance, a sign of the model's resilience and good generalization.
| S-EPMC11300600 | biostudies-literature
Project description:The PRINTS database, now in its 21st year, houses a collection of diagnostic protein family 'fingerprints'. Fingerprints are groups of conserved motifs, evident in multiple sequence alignments, whose unique inter-relationships provide distinctive signatures for particular protein families and structural/functional domains. As such, they may be used to assign uncharacterized sequences to known families, and hence to infer tentative functional, structural and/or evolutionary relationships. The February 2012 release (version 42.0) includes 2156 fingerprints, encoding 12 444 individual motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. Here, we report the current status of the database, and introduce a number of recent developments that help both to render a variety of our annotation and analysis tools easier to use and to make them more widely available. Database URL: www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/.
| S-EPMC3326521 | biostudies-literature
Project description:P-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids, and lipid-like molecules. Because of its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance. Although P-gp is one of the most studied ABC transporters, the mechanism by which its substrates access the cavity remains unclear. In this study, we perform coarse-grained molecular dynamics simulations to explore possible lipid access pathways in the inward-facing conformation of P-gp embedded in bilayers of different lipid compositions. In the inward-facing orientation, only lipids from the lower leaflet access the cavity of the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid-binding sites at the portals and within the cavity, which is in good agreement with previous experimental studies. This work includes several examples of lipid pathways for phosphatidylcholine and phosphatidylethanolamine lipids that help elucidate the molecular mechanism of lipid binding in P-gp.
| S-EPMC5839720 | biostudies-literature
Project description:The energy landscape of biomolecular systems contains many local minima that are separated by high energy barriers. Sampling this landscape in molecular dynamics simulations is a challenging task and often requires the use of enhanced sampling techniques. Here, we increase the sampling efficiency by coupling the fine-grained (FG) GROMOS force field to the coarse-grained (CG) Martini force field via the Hamiltonian replica exchange method (HREM). We tested the efficiency of this procedure using a lutein/octane system. In traditional simulations, cis-trans transitions of lutein are barely observed due to the high energy barrier separating these states. However, many of these transitions are sampled with our HREM scheme. The proposed method offers new possibilities for enhanced sampling of biomolecular conformations, making use of CG models without compromising the accuracy of the FG model.
| S-EPMC7426904 | biostudies-literature
Project description:In spite of its acoustic diversity, the speech signal presents statistical regularities that can be exploited by biological or artificial systems for efficient coding. Independent Component Analysis (ICA) revealed that on small time scales (∼ 10 ms), the overall structure of speech is well captured by a time-frequency representation whose frequency selectivity follows the same power law in the high frequency range 1-8 kHz as cochlear frequency selectivity in mammals. Variations in the power-law exponent, i.e. different time-frequency trade-offs, have been shown to provide additional adaptation to phonetic categories. Here, we adopt a parametric approach to investigate the variations of the exponent at a finer level of speech. The estimation procedure is based on a measure that reflects the sparsity of decompositions in a set of Gabor dictionaries whose atoms are Gaussian-modulated sinusoids. We examine the variations of the exponent associated with the best decomposition, first at the level of phonemes, then at an intra-phonemic level. We show that this analysis offers a rich interpretation of the fine-grained statistical structure of speech, and that the exponent values can be related to key acoustic properties. Two main results are: i) for plosives, the exponent is lowered by the release bursts, concealing higher values during the opening phases; ii) for vowels, the exponent is bound to formant bandwidths and decreases with the degree of acoustic radiation at the lips. This work further suggests that an efficient coding strategy is to reduce frequency selectivity with sound intensity level, congruent with the nonlinear behavior of cochlear filtering.
| S-EPMC7083313 | biostudies-literature
Project description:Transient receptor potential canonical 3 (TRPC3) channel belongs to the superfamily of transient receptor potential (TRP) channels which mediate Ca2+ influx into the cell. These channels constitute essential elements of cellular signalling and have been implicated in a wide range of diseases. TRPC3 is primarily gated by lipids and its surface expression has been shown to be dependent on cholesterol, yet a comprehensive exploration of its interaction with this lipid has thus far not emerged. Here, through 80 µs of coarse-grained molecular dynamics simulations, we show that cholesterol interacts with multiple elements of the transmembrane machinery of TRPC3. Through our approach, we identify an annular binding site for cholesterol on the pre-S1 helix and a non-annular site at the interface between the voltage-sensor-like domain and pore domains. Here, cholesterol interacts with exposed polar residues and possibly acts to stabilise the domain interface.
| S-EPMC9313397 | biostudies-literature