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67 results for “molecular generation”
Molecular datasets from "SMILES-Based Deep Generative Scaffold Decorator for De-Novo Drug Design"
<p>Herein find the molecular datasets from "<a href="https://chemrxiv.org/articles/SMILES-Based_Deep_Generative_Scaffold_Decorator_for_De-Novo_Drug_Design/11638383">SMILES-Based Deep Generative Scaffold Decorator for De-Novo Drug Design</a>". These were generated with SMILES-based scaffold decorator generative models trained with two training sets (DRD2 and ChEMBL). These generative models require a partially-built molecule (scaffold) as input and output several possible completions for each scaffold. Each dataset corresponds to a model trained with the ChEMBL or DRD2 sets, wither multi-step (ms) or single-step (ss) and the provenance of the scaffolds (validation set, or non-dataset).</p> <p>The molecules generated are annotated with a set of descriptors. The DRD2 datasets have the predicted probability of each molecule to be active on DRD2 (p) obtained from a Random Forest model. The ChEMBL model's descriptors are related to the synthesizability of the molecules (see manuscript). Also, the datasets decorated from validation set scaffolds are annotated whether they are part of the validation set (in_validation).</p>
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 (as indicated in red circle) and the other C. sphaerospermum isolates deposited in GenBank (NCBI)
Fig. 4. Maximum likelihood tree generated using ITS1-5.8S-ITS2 in Morphological and molecular description of Pallisentis roparensis n. sp. (Acanthocephala: Quadrigyridae) infecting the freshwater cat fish Wallago attu from Ropar Wetland, Punjab, India
Fig. 4. Maximum likelihood tree generated using ITS1-5.8S-ITS2 gene sequence of Pallisentis roparensis and the sequences of related taxa downloaded from GenBank. Numbers near internal nodes show ML bootstrap clade frequencies.
Fig. 3. Maximum likelihood tree generated using 28S in Morphological and molecular description of Pallisentis roparensis n. sp. (Acanthocephala: Quadrigyridae) infecting the freshwater cat fish Wallago attu from Ropar Wetland, Punjab, India
Fig. 3. Maximum likelihood tree generated using 28S rRNA gene sequence of Pallisentis roparensis and the sequences of related taxa downloaded from GenBank. Numbers near internal nodes show ML bootstrap clade frequencies.
Fig. 2. Maximum likelihood tree generated using 18S in Morphological and molecular description of Pallisentis roparensis n. sp. (Acanthocephala: Quadrigyridae) infecting the freshwater cat fish Wallago attu from Ropar Wetland, Punjab, India
Fig. 2. Maximum likelihood tree generated using 18S rRNA gene sequence of Pallisentis roparensis and the sequences of related taxa downloaded from GenBank. Numbers near internal nodes show ML bootstrap clade frequencies.
Source Data for the paper: "Quantum-classical simulations reveal the photoisomerization mechanism of a prototypical first-generation molecular motor"
<p>This dataset contains the raw data for the results shown in the paper.</p> <p>For each figure of the paper (main text), one directory with data file(s) is provided.</p>
Supplementary videos for "Active flow network generates molecular transport by packets: case of the endoplasmic reticulum"
<p>Videos showing simulated motion on the active flow network for different switching timescales. In particular, compare <span class="math-tex">\(\tau_{\text{switch}} = 3 \text{ s}\)</span> to <span class="math-tex">\(\tau_{\text{switch}} = 30 \text{ ms}\)</span>. The red bubbles are proportional to the number of particles present in a node. Initially, all particles are placed in a central source node.</p>
Reproducibility of "Diffusion-based Generative AI for Exploring Transition States from 2D Molecular Graphs"
<p>This file is the source data to ensure reproducibility of the paper "Diffusion-based Generative AI for Exploring Transition States from 2D Molecular Graphs". It contains the logs and results of all DFT calculations associated with transition states generated using the model proposed in the paper. It also includes code to reproduce the core findings of the paper, which can be done by running reproduce.sh. To accurately reproduce the results of the paper, use the v1.0.0 virtual environment from "https://github.com/seonghann/tsdiff".</p>
Coarse-Grained and Multi-Dimensional Data-Driven Molecular Generation: A Structure-Based Framework for Selective Inhibitor Design and Optimization
<p><span>Many approaches not only fail to consider the intricate binding pocket interactions, leading to molecules with suboptimal properties and stability, but also struggle with designing selective inhibitors. To address this challenge, we have developed an innovative structure-based three-dimensional molecular generation framework named </span><span>Coarse-grained and Multi-dimensional Data-driven molecular generation (CMD-GEN). This framework bridges three-dimensional ligand-protein complex data with two-dimensional drug-like molecule data by utilizing coarse-grained pharmacophore points sampled from diffusion models, thereby enriching the training data for generative models.</span> <span>Through a hierarchical architecture, it decomposes the generation of three-dimensional molecules within the pocket into sampling of coarse-grained pharmacophore points, generating of chemical structures, and alignment of conformations, avoiding the instability issues associated with inherent in deep generative model-based generation of molecular conformations.<br><br>This project provide the source dataset used to train and evaluate the overall model.<br></span></p>
Nanoporous carbon structures of different densities generated through GAP molecular dynamics
<p>These nanoporous (NP) carbon atomic structures, in extendend XYZ format, have been generated using a melt-graphitization-quench molecular dynamics (MD) protocol using a Gaussian interatomic potential (GAP) for amorphous carbon [1]. Simulation details and characterization of structural and mechanical properties will follow shortly in a scientific paper.</p> <p><strong>References</strong></p> <p>[1] M.A. Caro. GAP interatomic potential for amorphous carbon (2.0) [Data set]. Zenodo, 10.5281/zenodo.5243184 (2021).</p>
Molecular dynamics-generated ensemble dataset of ubiquitin; for "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles"
<p>The molecular dynamics-generated ensemble dataset (229Mb zip file) for ubiquitin, used in the manuscript "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles", submitted to the Journal of Chemical Information and Modeling (JCIM). The dataset consists of 6 .dcd files, and one .pdb file. </p>
AutoParams: An Automated Web-Based Tool To Generate Parameters for Molecular Dynamics Simulations
<p>Dataset of thirteen (13) compounds used to test the AutoParams webserver. Includes initial PDB files, generated parameters (mol2/frcmod files), and resulting AMBER-formatted MD inputs (prmtop/inpcrd). Additionally, includes 2D structure in PNG format and canonical SMILES string in .smi file format.</p>
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 in A taxonomic revision of Anthothela (Octocorallia: Scleraxonia: Anthothelidae) and related genera, with the addition of new taxa, using morphological and molecular data
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 of Anthothela-like specimens. Bayesian posterior probabilities shown above branch, ML bootstrap values below branch; HKY+G (Bayesian results split freq = 0.0019, 10000000 gen, burnin=25000). (* indicates nodes present only in Bayesian analysis).
FIGURE 5. The COI PCR amplicons generated via LepF1-LepR1 in First record of the genus Haritalodes Warren, 1890 and H. derogata (Fabricius, 1775) (Lepidoptera: Crambidae: Spilomelinae) from Türkiye and its morphological and molecular identification
FIGURE 5. The COI PCR amplicons generated via LepF1-LepR1 (Lanes 1-2), LCO1490-HCO2198 (Lanes 3-4), and Jerry-Pat (Lanes 5-6) primer pairs using DNA from the larvae (L) or adult (A) at 1% agarose gel. L refers to ladder (100 bp ladder marker, Invitrogen, USA).
AMCG: a graph dual atomic-molecular conditional molecular generator
<p>This repository contains the weights and the training datasets related to the paper</p> <p><a href="https://iopscience.iop.org/article/10.1088/2632-2153/ad5bbf" target="_blank" rel="noopener">AMCG: a graph dual atomic-molecular conditional molecular generator</a>, C. Abate, S. Decherchi, A. Cavalli.</p> <p> </p> <p>The code repository is available at <a href="https://github.com/carloabate/AMCG" target="_blank" rel="noopener">https://github.com/carloabate/AMCG</a></p>
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
FIGURE 13.Maximum Likelihood consensus tree generated from the 28S in A revision of the genus Isotomurus (Collembola: Isotomidae) in northern Iran using molecular evidence
FIGURE 13.Maximum Likelihood consensus tree generated from the 28S gene dataset with the GTR+I+G model. Bootstrap values more than 60% are given for appropriate clades; newly obtained sequences are in bold letters, others are from GenBank (NCBI).
Supplementary Table S1 and Supplementary Table S2 - Part of "Next generation leishmanization: revisiting molecular targets for selecting genetically engineered live-attenuated Leishmania"
<p>Supplementary Table S1 and Supplementary Table S2 -</p> <p>Part of "Next generation leishmanization: revisiting molecular targets for selecting genetically engineered live-attenuated Leishmania"</p>
Development of a Next Generation Sequencing (NGS) -Based Assay to Detect Preeclampsia Molecular Markers
ClinicalTrials.gov study NCT02808494. IPD Sharing: NO. Countries: 1. Publications: 1.
To Investigate the Molecular Mechanism of Traditional Chinese Medicine Constitution Using Next-generation Sequencing in Nasopharyngeal Carcinoma
ClinicalTrials.gov study NCT03578575. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.