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14 results for “HADDOCK”
Haddock Data
<p>Dataset containing all archaeological sites in Europe where haddock (Melanogrammus aeglefinus) has been found, and all the fish remains from these sites, based on published and unpublished species identifications.</p>
HADDOCK file I/O benchmark
<p>The benchmark is composed of 1,000,000 structures in PDB format extracted from the results of applying HADDOCK to the cases of the Protein-Protein Docking Benchmark v5 (BM5), which is a well-accepted benchmark in the protein docking community. Due to the nature of the BM5 benchmark, the PDB files are different in length as they represent different molecular structures. Files are placed in a single directory and named according to the BM5 they originated from, docking procedure used, docking stage and model number, example; <em>1BVN_ti5-it1_167.pdb </em>and<em> 1AK4_cm-it0_1601.pdb</em>. The HADDOCK file I/O benchmark is related to our BioExcel project on <em><a href="https://bioexcel.eu/research/projects/high-throughput-modelling-of-interactomes/">high throughput modelling of interactomes</a></em>, this task will generate a gargantuan number of files and will only be possible by taking advantage of exascale computing resources both for processing and I/O handling.</p>
HADDOCK screening against the COVID-19 RNA dependent RNA polymerase (RdRp)
<p>The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process.</p> <p>One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use.</p> <p>Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) that plays an essential role in the virus replication process by screening ~2000 approved drugs (and 6 experimental ones) against this particular protein.</p> <p>This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations:</p> <ul> <li><a href="https://zenodo.org/record/3929438">Mpro: Shape-based assay</a></li> <li><a href="https://zenodo.org/record/3929446">Mpro: Pharmacophore-based assay</a></li> <li><a href="https://zenodo.org/record/3929463">ACE2</a></li> </ul> <p>More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.</p>
HADDOCK screening against human Angiotensin Converting Enzyme 2 (ACE2)
<p>The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process.</p> <p>One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use.</p> <p>Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the Angiotensin Converting Enzyme 2 receptor (ACE2) that acts as one of the main gateways for viral entry in the host cell. We have screened ~2000 compounds against the inhibitor-bound closed form of the receptor.</p> <p>This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations:</p> <ul> <li><a href="https://zenodo.org/record/3929438">Mpro: Shape-based assay</a></li> <li><a href="https://zenodo.org/record/3929446">Mpro: Pharmacophore-based assay</a></li> <li><a href="https://zenodo.org/record/3929449">RdRp</a></li> </ul> <p>More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.</p>
HADDOCK pharmacophore-based screening against the COVID-19 main protease (Mpro)
<p>The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process.</p> <p>One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use.</p> <p>Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the SARS-CoV-2 main protease (3CLpro) that plays an essential role in the virus replication process by screening ~2000 approved drugs (and 6 experimental ones) against this particular protein using a pharmacophore-based assay.</p> <p>This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations:</p> <ul> <li><a href="https://zenodo.org/record/3929438">Mpro: Shape-based assay</a></li> <li><a href="https://zenodo.org/record/3929463">ACE2</a></li> <li><a href="https://zenodo.org/record/3929449">RdRp</a></li> </ul> <p>More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.</p>
HADDOCK shape-based screening against the COVID-19 main protease (Mpro)
<p>The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process.</p> <p>One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use.</p> <p>Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the SARS-CoV-2 main protease (3CLpro) that plays an essential role in the virus replication process by screening ~2000 approved drugs (and 6 experimental ones) against this particular protein using a shape-based assay.</p> <p>This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations:</p> <ul> <li><a href="https://zenodo.org/record/3929446">Mpro: Pharmacophore-based assay</a></li> <li><a href="https://zenodo.org/record/3929463">ACE2</a></li> <li><a href="https://zenodo.org/record/3929449">RdRp</a></li> </ul> <p>More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.</p>
HADDOCK Coarse-Grained Protein-DNA Docking Dataset
<p>This dataset is the result of the benchmarking done in the publication <a href="https://www.frontiersin.org/articles/10.3389/fmolb.2019.00102/full"><em>MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing</em></a> in which HADDOCK's coarse-grain support is extended to Protein-DNA docking.</p> <p>It contains both the All-atom and Coarse-Grained output of 46 macromolecular complexes derived from the <a href="https://haddock.science.uu.nl/dna/benchmark.html">Protein-DNA benchmark</a> (<a href="https://doi.org/10.1093/nar/gkn386">10.1093/nar/gkn386</a>) as well as 6 complexes with experimental information, CAPRI Target 95 (PRC1 ubiquitination module bound to the nucleosome) and all new parameters added to HADDOCK.</p>
Genetic structuring in Atlantic haddock contrasts with current management regimes
<div class="WordSection1"> <p><span><span><span><span><span><span><span><span><span><span><span><span>The advent of novel genetic methods has made it possible to investigate population structure and connectivity in mobile marine fish species: knowledge of which is essential to ensure a sustainable fishery. Haddock (<i>Melanogrammus aeglefinus</i>) is a highly exploited marine teleost distributed along the coast and continental shelf on both sides of the North Atlantic Ocean. However, little is known about its population structure. Here, we present the first study using single nucleotide polymorphism markers to assess the genetic population structure of haddock at multiple geographic scales, from the transatlantic to the local (fjord) level. Genotyping 138 SNP loci in 1329 individuals from 19 locations across the North Atlantic revealed three main genetic clusters, consisting of a Northwest Atlantic-, a Northeast Arctic- and a Northeast Atlantic cluster. We also observed a genetically distinct fjord population and a pattern of isolation-by-distance in the Northeast Atlantic. Our results contrast with the current management regime for this species in the Northeast Atlantic, as we found structure within some management areas. The study adds to the growing recognition of population structuring in marine organisms in general, and fishes in particular, and is of clear relevance for management of haddock in the Northeast Atlantic.</span></span></span></span></span></span></span></span></span></span></span></span></p> </div>
Genetic structuring in Atlantic haddock contrasts with current management regimes
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Figure 4 from: Drazen JC, Smith CR, Gjerde K, Au W, Black J, Carter G, Clark M, Durden JM, Dutrieux P, Goetze E, Haddock S, Hatta M, Hauton C, Hill P, Koslow J, Leitner AB, Measures C, Pacini A, Parrish F, Peacock T, Perelman J, Sutton T, Taymans C, Tunnicliffe V, Watling L, Yamamoto H, Young E, Ziegler AF (2019) Report of the workshop Evaluating the nature of midwater mining plumes and their potential effects on midwater ecosystems. Research Ideas and Outcomes 5: e33527. https://doi.org/10.3897/rio.5.e33527
Figure 4 The mesopelagic ecoregions or biogeographic provinces of the world's oceans proposed by Sutton et al. (2017), available under a CC BY 4.0 license. The numbers are simply for reference, and relate to the geographical names referenced in the paper and in the workshop discussion below. Areas with depths less than 200 m shaded in black.
Figure 3 from: Drazen JC, Smith CR, Gjerde K, Au W, Black J, Carter G, Clark M, Durden JM, Dutrieux P, Goetze E, Haddock S, Hatta M, Hauton C, Hill P, Koslow J, Leitner AB, Measures C, Pacini A, Parrish F, Peacock T, Perelman J, Sutton T, Taymans C, Tunnicliffe V, Watling L, Yamamoto H, Young E, Ziegler AF (2019) Report of the workshop Evaluating the nature of midwater mining plumes and their potential effects on midwater ecosystems. Research Ideas and Outcomes 5: e33527. https://doi.org/10.3897/rio.5.e33527
Figure 3 Clockwise from top left: Benthocodon jelly credit MBARI, Viperfish credit Jeff Drazen, Lanternfish credit Jeff Drazen, Appendicularian and mucus house credit MBARI, Cranchiid squid credit MBARI, Sapphirina copepod credit Erica Goetze/Katja Peijnenburg.
Figure 1 from: Drazen JC, Smith CR, Gjerde K, Au W, Black J, Carter G, Clark M, Durden JM, Dutrieux P, Goetze E, Haddock S, Hatta M, Hauton C, Hill P, Koslow J, Leitner AB, Measures C, Pacini A, Parrish F, Peacock T, Perelman J, Sutton T, Taymans C, Tunnicliffe V, Watling L, Yamamoto H, Young E, Ziegler AF (2019) Report of the workshop Evaluating the nature of midwater mining plumes and their potential effects on midwater ecosystems. Research Ideas and Outcomes 5: e33527. https://doi.org/10.3897/rio.5.e33527
Figure 1 Front row left to right: Jeff Drazen, Pierre Dutrieux, Les Watling, Astrid Leitner, Emily Young, Verena Tunnicliffe. Second row: Chris Measures, Mariko Hatta, Jessica Perelman, Erica Goetze, Jen Durden, Celine Taymans. Third row: Hiroyuki Yamamoto, Kristina Gjerde, Paul Hill, Amanda Ziegler, Chris Hauton, Tracey Sutton. Back row: Steve Haddock, Malcolm Clark, Tom Peacock, Tony Koslow, Craig Smith. Not Pictured: Whit Au, Jesse Black, Frank Parrish, Aude Pacini.
Molecular Dynamics Simulations of HADDOCK-predicted Complex Structures of apoE2 and Factor H
<p>Input and output data for the molecular dynamics simulations of the FH5–7/ApoE2 complex. Initial structures generated with the HADDOCK v2.4 web server with 3 nm distance restraints for lysine pairs that were experimentally found to be cross-linked with DSS. </p> <p>Five clusters and the four representative structures provided by HADDOCK were then used for atomistic molecular dynamics simulations. These structures were solvated and simulated with both CHARMM36m and Amber FF14SB force fields for 250 ns each using GROMACS 2021. The recommended simulation parameters were used for both force fields, and they are available in the mdp files. </p> <p>For each of these 5 (clusters) x 4 (structures per cluster) x 2 (force fields) = 40 simulations, the outputs and inputs are provided; the trajectory (xtc), energy file (edr), final structure (gro), run parameter file (tpr), and continue point (cpt) are system-specific, whereas a single topology (top) and index file (ndx) is shared among all simulations with the same force field. The molecule definitions (itp) referred to in the topology are provided in the compressed files.</p>
Figure 2 from: Drazen JC, Smith CR, Gjerde K, Au W, Black J, Carter G, Clark M, Durden JM, Dutrieux P, Goetze E, Haddock S, Hatta M, Hauton C, Hill P, Koslow J, Leitner AB, Measures C, Pacini A, Parrish F, Peacock T, Perelman J, Sutton T, Taymans C, Tunnicliffe V, Watling L, Yamamoto H, Young E, Ziegler AF (2019) Report of the workshop Evaluating the nature of midwater mining plumes and their potential effects on midwater ecosystems. Research Ideas and Outcomes 5: e33527. https://doi.org/10.3897/rio.5.e33527
Figure 2 The principle midwater ecosystems across depth and some pertinent characteristics of each.
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