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30 results for “interaction interface”
Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical calculations
<p>Allosteric modulators are called to be promising candidates in G protein-coupled receptor (GPCR) drug development by displaying target selectivity and fewer side effects. Among the allosteric sites known to date, extrahelical cavities represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability; the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze the dynamics and interactions in the PAR2, C5aR1, and GCGR receptors unbound and bound to allosteric modulators at the receptor-lipid interface using molecular dynamics simulations in three lipid compositions. In addition, we performed quantum chemical calculations to further explore electrostatic interactions and the strength of atom pairwise contacts in the stabilization of the ligand-receptor complexes. We show that besides classical hydrogen bonds weak polar interactions such as O-HC, O-Br, and S-HC contacts and aromatic interactions contribute to the binding of allosteric modulators at the extrahelical sites in the middle of the membrane. The allosteric cavities are open and detectable in various membrane compositions but not always predicted as druggable. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from the simulations. Although ligand-lipid interactions are weak, the lipid tails play a role in sizing and shaping the large part of the allosteric cavity. </p> <p>You will find the following files:</p> <ul> <li>Input files of the equilibration and production protocols of MD simulations (MD_simulations_inputs.zip)</li> <li>Input files and coordinate files of F-SAPT and NCIPLOT calculations (quantum_chemical_coordiates_inputs.zip)</li> </ul>
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction
<p>This dataset contains replication data for the paper titled "DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction". The dataset consists of pickled Pandas DataFrame files, along with training, validation, and (for DB5-Plus) test filename lists for cross-validation, that can be used to develop and evaluate protein interface prediction models. This dataset also contains the externally generated residue-level PSAIA and HH-suite3 features for users' convenience (e.g. raw MSAs and profile HMMs for each protein complex). Our GitHub repository linked in the "Additional notes" metadata section below provides more details on how we parsed through these files to create our cross-validation datasets. The GitHub repository for DIPS-Plus also includes scripts that can be used to impute missing feature values and convert the final "raw" complexes into DGL-compatible graph objects. Since our final DGL graph representation for each complex uses PyTorch tensors in its construction of residue embeddings, the final representation of each complex can easily be adapted to fit the users' needs (e.g. feeding a complex's 2D residue feature tensors into a convolutional neural network).</p>
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction (Supplementary Data)
<p>This dataset contains supplementary replication data for the paper titled "DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction". In particular, it contains a new version of our `final_raw_dips.tar.gz` protein pair representations which now contain (1) residue-level annotations for intrinsic disorder regions (IDRs) as well as (2) a copy of each protein pair representation in the HDF5 file format for programming language-agnostic read capabilities. In addition, this record also contains (3) raw MSAs (in HDF5 file format) generated for each protein pair using Jackhmmer and AlphaFold's small version of the Big Fantastic Database (BFD). Lastly, this record contains (4) PDB metadata derived for each DIPS-Plus complex using Graphein's PDBManager API as well as (5) structure-based (i.e., FoldSeek-based) training and validation splits of the dataset's complexes in the form of respective text files containing the file paths of complexes assigned to each split.</p>
RAW DATA - Control of Intermolecular Interactions toward the Production of Free-Standing Interfacial Polydopamine Films - ACS Applied Materials & Interfaces 2023 15 (30), 36922-36935 DOI: 10.1021/acsami.3c05236
<div>This repository contains RAW data for the experiment described in the publication:</div> <div> </div> <div>Jakub Szewczyk, Visnja Babacic, Adam Krysztofik, Olena Ivashchenko, Mikołaj Pochylski, Robert Pietrzak, Jacek Gapiński, Bartłomiej Graczykowski, Mikhael Bechelany, and Emerson Coy, Control of Intermolecular Interactions toward the Production of Free-Standing Interfacial Polydopamine Films, ACS Applied Materials & Interfaces 2023 <em>15</em> (30), 36922-36935, DOI: 10.1021/acsami.3c05236.</div> <div> </div> <div>For more information please contact the corresponding authors.</div>
Dataset for article: Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes
<p>Proteins involved in interactions throughout the course of evolution tend to co-evolve and compensatory changes may occur in interacting proteins to maintain or refine such interactions. However, certain residue pair alterations may prove to be detrimental for functional interactions. Hence, determining co-evolutionary pairings that could be structurally or functionally relevant for maintaining the conservation of an inter-protein interaction is important. Inter-protein co-evolution analysis in several complexes utilizing multiple existing methodologies suggested that co-evolutionary pairings can occur in spatially proximal and distant regions in inter-protein interactions. Subsequently, the Co-Var (<b>Co</b>rrelated <b>Var</b>iation) method based on mutual information and Bhattacharyya coefficient was developed, validated, and found to perform relatively better than CAPS and EV-complex. Interestingly, while applying the Co-Var measure and EV-complex program on a set of protein-protein interaction complexes, co-evolutionary pairings were obtained in interface and non-interface regions in protein complexes. The Co-Var approach involves determining high degree co-evolutionary pairings that include multiple co-evolutionary connections between particular co-evolved residue positions in one protein with multiple residue positions in the binding partner. Detailed analyses of high degree co-evolutionary pairings in protein-protein complexes involved in cancer metastasis suggested that most of the residue positions forming such co-evolutionary connections mainly occurred within functional domains of constituent proteins and substitution mutations were also common among these positions. The physiological relevance of these predictions suggests that Co-Var can predict residues that could be crucial for preserving functional protein-protein interactions. Finally, <b>Co-Var </b>web server (<a href="http://www.hpppi.iicb.res.in/ishi/covar/index.html">http://www.hpppi.iicb.res.in/ishi/covar/index.html</a>) that implements this methodology identifies co-evolutionary pairings in intra and inter-protein interactions.</p>
Dataset for article: Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes
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Data from: Heterospecific mating interactions as an interface between ecology and evolution
<p>Reproductive interference (costly interspecific sexual interactions) are well-understood to promote divergence in mating-relevant traits (i.e. reproductive character displacement: RCD), but it can also reduce population growth, eventually leading to local extinction of one of the species. The ecological and evolutionary processes driven by reproductive interference can interact with each other. These interactions are likely to influence whether the outcome is co-existence or extinction, but remain little studied. In this paper, we first develop an eco-evolutionary perspective on reproductive interference by integrating ecological and evolutionary processes in a common framework. We also present a simple model to demonstrate the eco-evolutionary dynamics of reproductive interference. We then identify a number of factors that are likely to influence the relative likelihoods of extinction or RCD. We discuss particularly relevant factors by classifying them into four categories: the nature of the traits responding to selection, the mechanisms determining the expression of these traits, mechanisms of reproductive interference, and the ecological background. We highlight previously underappreciated ways in which these factors may influence the relative likelihoods of RCD and local extinction. By doing so, we also identify questions and future directions that will increase our holistic understanding of the outcomes of reproductive interference.</p>
Research Data For "Structure and Interactions at the Mg(0001)/Water Interface: An ab initio Study" Paper
<p>This folder contains data used in the paper "Structure and Interactions at the Mg/Water Interface: An ab initio Study". Some details on the structure are as follows:</p> <p>The folder "figures" contains data to create various figures in the main paper.</p> <p>The folder "md_traj" contains the molecular dynamics trajectory. The file "traj.exyz" is a standard format which can be opened with various software. "traj.json" contains the same information in an in-house format used by the author. The "thermo_data.json" contains various thermodynamics properties over the simulation, such as temperatures and kinetic energies. Units are femtoseconds, Angstrom, electron-volts and Kelvin.</p> <p>The folders "mg_plus_clusters"/"mg_plus_monomer"/"misc_reference_structs" contain geometries for various structures used in the paper (in *.exyz format). These also contain *.json files; these contain information on how the calculations were carried out in a format used by the author (they are small files primarily included for the benefit of the author).</p> <p> </p>
Predictive Executive Functioning Models Using Interactive Tangible-Graphical Interface Devices
ClinicalTrials.gov study NCT01711372. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants
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Data from: Heterospecific mating interactions as an interface between ecology and evolution
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Data from: Human–Cougar interactions in the wildland–urban interface of Colorado's front range
As human populations continue to expand across the world, the need to understand and manage wildlife populations within the wildland–urban interface is becoming commonplace. This is especially true for large carnivores as these species are not always tolerated by the public and can pose a risk to human safety. Unfortunately, information on wildlife species within the wildland–urban interface is sparse, and knowledge from wildland ecosystems does not always translate well to human‐dominated systems. Across western North America, cougars (Puma concolor) are routinely utilizing wildland–urban habitats while human use of these areas for homes and recreation is increasing. From 2007 to 2015, we studied cougar resource selection, human–cougar interaction, and cougar conflict management within the wildland–urban landscape of the northern Front Range in Colorado, USA. Resource selection of cougars within this landscape was typical of cougars in more remote settings but cougar interactions with humans tended to occur in locations cougars typically selected against, especially those in proximity to human structures. Within higher housing density areas, 83% of cougar use occurred at night, suggesting cougars generally avoided human activity by partitioning time. Only 24% of monitored cougars were reported for some type of conflict behavior but 39% of cougars sampled during feeding site investigations of GPS collar data were found to consume domestic prey items. Aversive conditioning was difficult to implement and generally ineffective for altering cougar behaviors but was thought to potentially have long‐term benefits of reinforcing fear of humans in cougars within human‐dominated areas experiencing little cougar hunting pressure. Cougars are able to exploit wildland–urban landscapes effectively, and conflict is relatively uncommon compared with the proportion of cougar use. Individual characteristics and behaviors of cougars within these areas are highly varied; therefore, conflict management is unique to each situation and should target individual behaviors. The ability of individual cougars to learn to exploit these environments with minimal human–cougar interactions suggests that maintaining older age structures, especially females, and providing a matrix of habitats, including large connected open‐space areas, would be beneficial to cougars and effectively reduce the potential for conflict.
Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA
<p><span>Tree spatial patterns in dry coniferous forests of the western US, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre-existing forest structure shapes tree spatial patterns is limited. In this study, we (1) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and (3) examined tree spatial patterns of live trees before and after fire, and of fire-killed trees. Tree mortality in the historical period was clustered and density-dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, post-fire tree patterns were more uniform and devoid of moderately sized tree groups. Post-fire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western US. This divergence suggests that decades of forest dynamics without significant disturbances has altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.</span></p>
Data for manuscript: An all-atom view into the disordered interaction interface of the TRIM5alpha PRYSPRY domain and the HIV capsid
<p>The data is provided as a part of the manuscript "<strong>An all-atom view into the disordered interaction interface of the TRIM5alpha PRYSPRY domain and the HIV capsid</strong>". </p> <p>This repository includes an archive with folders:</p> <div> </div> <div>MDData</div> <div>-- Contains shortened versions of the MD trajectories, and initial structure files used to run simulations</div> <div> </div> <div>FigureData </div> <div>-- Contains comma separated value files for each figure</div>
Data from: Human–Cougar interactions in the wildland–urban interface of Colorado's front range
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Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA
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Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood based method to covary across protein-protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex provided that the number of aligned sequences is greater than the average of the lengths of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.
Predictive Executive Functioning Models Using Interactive Tangible-Graphical Interface Devices in Adults
ClinicalTrials.gov study NCT02127931. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface
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Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.