Search Results - "https :// github"
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Authors: et al.
Subject Terms: Biochemistry, Genetics, Pharmacology, Biotechnology, Cancer, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, significantly attenuate fibrosis, screen active compounds, presents significant challenges, https :// github, 8 å ), drug discovery community, discover critical targets, accelerating drug discovery, structurally relevant targets, 50 , relevant targets, therapeutic discovery, would benefit, source software, revealed retinoid, ray crystallography, prioritize disease, murine models, findings demonstrated, fibrotic cascades
Availability: https://doi.org/10.1021/acs.jmedchem.5c01682.s001
https://figshare.com/articles/journal_contribution/ComplexDnet_A_Network-Based_Strategy_to_Discover_Critical_Targets_and_Screen_Active_Compounds_for_Complex_Diseases/30053034 -
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Authors:
Subject Terms: Biochemistry, Biotechnology, Mental Health, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, transformer encoder architecture, substantially outperforming msbert, reasonable spectral embeddings, quality spectral embeddings, offered new solutions, mtbls1572 data set, mona data set, https :// huggingface, https :// github, gnps training subset, gnps test subset, dimensional vector representations, 1 hit ratio, experimental results show, specembedding significantly enhances, employs replicated spectra, experimental conditions, widely applied, web service, specembedding achieves, source code, recent advancements, publicly available
Relation: https://figshare.com/articles/journal_contribution/Supervised_Contrastive_Learning_Leads_to_More_Reasonable_Spectral_Embeddings/30118561
Availability: https://doi.org/10.1021/acs.analchem.5c02655.s001
https://figshare.com/articles/journal_contribution/Supervised_Contrastive_Learning_Leads_to_More_Reasonable_Spectral_Embeddings/30118561 -
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Authors: et al.
Subject Terms: Microbiology, Biotechnology, Inorganic Chemistry, Science Policy, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, supporting rational decision, source code provided, minimal input requirements, microaerobic production stage, maximizing bioprocess efficiency, https :// github, https :// chemnettools, exponential feeding strategies, friendly web tool, batch fermentation strategies, arrested production stage, aid process design, extensive modeling expertise, demonstrate fedbatchdesigner ’, process ’, friendly dashboard, batch processes, arrested fed, saccharomyces cerevisiae, present fedbatchdesigner, optimizing fed, nitrogen starvation, mit license, mathematical modeling
Availability: https://doi.org/10.1021/acssynbio.5c00357.s002
https://figshare.com/articles/journal_contribution/Fedbatchdesigner_A_User-Friendly_Dashboard_for_Modeling_and_Optimizing_Growth-Arrested_Fed-Batch_Processes/29614871 -
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Authors:
Subject Terms: Medicine, Biotechnology, Cancer, Virology, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, significantly outperforming state, multimodal information fusion, https :// github, enabling knowledge transfer, convolutional neural networks, process molecular images, molecular images demonstrate, benchmark data sets, transfer learning strategy, providing significant assistance, deep residual network, predict molecular carcinogenicity, molecular feature extraction, carcinogenicity data set, molecular carcinogenicity, deep learning, data quality, significant improvement, feature richness, carcinogenicity prediction, visually observing
Availability: https://doi.org/10.1021/acs.jcim.5c01362.s001
https://figshare.com/articles/journal_contribution/MMF-MCP_A_Deep_Transfer_Learning_Model_Based_on_Multimodal_Information_Fusion_for_Molecular_Feature_Extraction_and_Carcinogenicity_Prediction/29646590 -
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Authors: et al.
Subject Terms: Biochemistry, Medicine, Molecular Biology, Sociology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, various data sets, processing functional groups, identify functional group, https :// github, carbon backbone ), functional group level, specific molecular patterns, molecular structure comparison, accfg generates refined, molecular structures, molecular pairs, molecular modality, level differences, useful tool, tool designed, textual descriptors, results demonstrate, present accfg, molecules based, molecule ’, manual examination
Relation: https://figshare.com/articles/journal_contribution/AccFG_Accurate_Functional_Group_Extraction_and_Molecular_Structure_Comparison/29850026
Availability: https://doi.org/10.1021/acs.jcim.5c01317.s001
https://figshare.com/articles/journal_contribution/AccFG_Accurate_Functional_Group_Extraction_and_Molecular_Structure_Comparison/29850026 -
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Authors: et al.
Subject Terms: Biochemistry, Medicine, Molecular Biology, Sociology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, various data sets, processing functional groups, identify functional group, https :// github, carbon backbone ), functional group level, specific molecular patterns, molecular structure comparison, accfg generates refined, molecular structures, molecular pairs, molecular modality, level differences, useful tool, tool designed, textual descriptors, results demonstrate, present accfg, molecules based, molecule ’, manual examination
Relation: https://figshare.com/articles/journal_contribution/AccFG_Accurate_Functional_Group_Extraction_and_Molecular_Structure_Comparison/29850029
Availability: https://doi.org/10.1021/acs.jcim.5c01317.s002
https://figshare.com/articles/journal_contribution/AccFG_Accurate_Functional_Group_Extraction_and_Molecular_Structure_Comparison/29850029 -
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Authors: et al.
Subject Terms: Biophysics, Molecular Biology, Cancer, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, within ± 0, vertical transition energies, rydberg transitions occurring, many computational methods, https :// github, deemed chemically accurate, corresponding data associated, associated github repository, quest also includes, accurate excitation energies, quest database, excitation character, vast majority, various single, states characterized, state methodologies, significant list, reported values, pvtz estimate, popular excited, particularly challenging, large number, hydrogen atoms
Availability: https://doi.org/10.1021/acs.jctc.5c00975.s001
https://figshare.com/articles/journal_contribution/QUEST_Database_of_Highly-Accurate_Excitation_Energies/29865870 -
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Authors: et al.
Subject Terms: Biophysics, Molecular Biology, Cancer, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, within ± 0, vertical transition energies, rydberg transitions occurring, many computational methods, https :// github, deemed chemically accurate, corresponding data associated, associated github repository, quest also includes, accurate excitation energies, quest database, excitation character, vast majority, various single, states characterized, state methodologies, significant list, reported values, pvtz estimate, popular excited, particularly challenging, large number, hydrogen atoms
Availability: https://doi.org/10.1021/acs.jctc.5c00975.s002
https://figshare.com/articles/journal_contribution/QUEST_Database_of_Highly-Accurate_Excitation_Energies/29865873 -
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Authors: et al.
Subject Terms: Biochemistry, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, reverse spectral search, principle first introduced, multiple precursor ions, library matching remains, https :// github, annotation workflows face, untargeted metabolomics data, benchmark data sets, tandem mass spectrometry, computationally efficient solution, chimeric spectral annotation, nonchimeric reference spectra, mass spectra, chimeric spectra, data reuse, overlooked solution, composite spectra, source codes, simultaneous fragmentation, reannotation strategies, reaching billions, public repositories, metabolite annotations, largely overlooked, gold standard, gnps ecosystem
Relation: https://figshare.com/articles/journal_contribution/Reverse_Spectral_Search_Reimagined_A_Simple_but_Overlooked_Solution_for_Chimeric_Spectral_Annotation/29922804
Availability: https://doi.org/10.1021/acs.analchem.5c02047.s001
https://figshare.com/articles/journal_contribution/Reverse_Spectral_Search_Reimagined_A_Simple_but_Overlooked_Solution_for_Chimeric_Spectral_Annotation/29922804 -
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Authors: Alison Felipe Alencar Chaves
Subject Terms: Biochemistry, Biotechnology, Developmental Biology, Inorganic Chemistry, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, traditional spreadsheet formats, throughput sample analyses, samplewise similarity metrics, local r setup, intuitively assessing large, https :// github, free data visualization, fastest computational platforms, based r application, visual quality control, rapid quality control, quality control metrics, peptide length distributions, fragpipe results fragpipe, protein data visualization, protein abundance discrepancies, scale proteomics data, quality scores, fragpipe introduced, filter peptide, protein coverage, version 23, spectrum matches
Relation: https://figshare.com/articles/journal_contribution/PSManalyst_A_Dashboard_for_Visual_Quality_Control_of_FragPipe_Results/29922914
Availability: https://doi.org/10.1021/acs.jproteome.5c00557.s002
https://figshare.com/articles/journal_contribution/PSManalyst_A_Dashboard_for_Visual_Quality_Control_of_FragPipe_Results/29922914 -
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Authors:
Subject Terms: Biophysics, Genetics, Biotechnology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, https :// github, disk space compared, artificial neural network, thus facilitating storage, large protein complexes, intrinsically disordered proteins, including folded proteins, bound protein systems, biomolecular simulation studies, compress md trajectories, simulation trajectories, biomolecular systems, share large, optimal storage, simulation programs, larger systems, composite systems, tested across, scientific community, remarkable stride, publicly available, practical solution, phospholipid bilayers
Relation: https://figshare.com/articles/journal_contribution/Employing_Artificial_Neural_Networks_for_Optimal_Storage_and_Facile_Sharing_of_Molecular_Dynamics_Simulation_Trajectories/29930872
Availability: https://doi.org/10.1021/acs.jcim.5c01294.s001
https://figshare.com/articles/journal_contribution/Employing_Artificial_Neural_Networks_for_Optimal_Storage_and_Facile_Sharing_of_Molecular_Dynamics_Simulation_Trajectories/29930872 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Cell Biology, Biotechnology, Hematology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, thereby promoting accessible, secondary structure probability, residue distance matrices, quality graphical outputs, packages often lack, ligand occupancy maps, https :// pypi, generate interactive plots, different temperatures illustrates, comparative tests performed, amyloid peptide simulations, online web server, principal component analysis, descriptive statistical analysis, based software package, web platform designed, https :// github, https :// dynamispectra, reproducible md analysis, reproducible analysis tools, python software package, web platform
Relation: https://figshare.com/articles/journal_contribution/DynamiSpectra_A_Python_Software_Package_and_Web_Platform_for_Molecular_Dynamics_Data_Analysis_in_Computational_Biology/29955680
Availability: https://doi.org/10.1021/acs.jcim.5c01270.s002
https://figshare.com/articles/journal_contribution/DynamiSpectra_A_Python_Software_Package_and_Web_Platform_for_Molecular_Dynamics_Data_Analysis_in_Computational_Biology/29955680 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Cell Biology, Biotechnology, Hematology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, thereby promoting accessible, secondary structure probability, residue distance matrices, quality graphical outputs, packages often lack, ligand occupancy maps, https :// pypi, generate interactive plots, different temperatures illustrates, comparative tests performed, amyloid peptide simulations, online web server, principal component analysis, descriptive statistical analysis, based software package, web platform designed, https :// github, https :// dynamispectra, reproducible md analysis, reproducible analysis tools, python software package, web platform
Relation: https://figshare.com/articles/journal_contribution/DynamiSpectra_A_Python_Software_Package_and_Web_Platform_for_Molecular_Dynamics_Data_Analysis_in_Computational_Biology/29955677
Availability: https://doi.org/10.1021/acs.jcim.5c01270.s001
https://figshare.com/articles/journal_contribution/DynamiSpectra_A_Python_Software_Package_and_Web_Platform_for_Molecular_Dynamics_Data_Analysis_in_Computational_Biology/29955677 -
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Authors:
Subject Terms: Biochemistry, Medicine, Immunology, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, uncover distinct regions, tunable solvation properties, new geometric measure, negligible vapor pressure, machine learning prediction, https :// github, dimensionality reduction techniques, dilution activity coefficients, analysis reveals many, traditional il selection, design space exploration, >- 125 ), develop machine learning, refrigerant separation involving, il design space, >- 410a separation, >- 125 solubility, >- 125, >- 410a, refrigerant mixtures, >- 32, widely used
Relation: https://figshare.com/articles/journal_contribution/Design_Space_Exploration_and_Machine_Learning_Prediction_of_Hydrofluorocarbon_Solubility_in_Ionic_Liquids_for_Refrigerant_Separation/29977765
Availability: https://doi.org/10.1021/acs.jcim.5c01216.s001
https://figshare.com/articles/journal_contribution/Design_Space_Exploration_and_Machine_Learning_Prediction_of_Hydrofluorocarbon_Solubility_in_Ionic_Liquids_for_Refrigerant_Separation/29977765 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Medicine, Hematology, Computational Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, one specific challenge, extensive human input, demo data sets, attracted increasing interest, cryptic site region, 93 cryptic pockets, studied cryptic sites, cryptic sites studies, cryptosite data set, 84 protein systems, procedure dynamically identifies, two cryptic sites, https :// github, dynamic pocket transitions, conformational dynamics capturing, based pocket characterization, wbc method outperforms, md simulation results, cryptic sites, two well
Availability: https://doi.org/10.1021/acs.jctc.5c01019.s001
https://figshare.com/articles/journal_contribution/Identification_of_Protein_Cryptic_Sites_via_Conformational_Dynamics_Capturing_and_Water-Based_Pocket_Characterization_in_Molecular_Dynamics_Simulations/30005528 -
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Authors:
Subject Terms: Biophysics, Biochemistry, Medicine, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, throughput screening due, needs without requiring, https :// github, automate microbial handling, recombinant protein production, source opentrons ot, 7 – 17, produce recombinant proteins, generating recombinant proteins, automated heterologous expression, automated protein expression, 2 hardware setup, protein expression, automated pipeline, minimal ot, 7 kb, time consumption
Relation: https://figshare.com/articles/journal_contribution/APEX_Automated_Protein_EXpression_in_Escherichia_coli/30037933
Availability: https://doi.org/10.1021/acssynbio.5c00189.s001
https://figshare.com/articles/journal_contribution/APEX_Automated_Protein_EXpression_in_Escherichia_coli/30037933 -
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Authors:
Subject Terms: Biophysics, Biochemistry, Medicine, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, throughput screening due, needs without requiring, https :// github, automate microbial handling, recombinant protein production, source opentrons ot, 7 – 17, produce recombinant proteins, generating recombinant proteins, automated heterologous expression, automated protein expression, 2 hardware setup, protein expression, automated pipeline, minimal ot, 7 kb, time consumption
Relation: https://figshare.com/articles/journal_contribution/APEX_Automated_Protein_EXpression_in_Escherichia_coli/30037939
Availability: https://doi.org/10.1021/acssynbio.5c00189.s002
https://figshare.com/articles/journal_contribution/APEX_Automated_Protein_EXpression_in_Escherichia_coli/30037939 -
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Authors:
Subject Terms: Biophysics, Biochemistry, Pharmacology, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, long computation times, ligand binding affinities, https :// github, drug discovery pipelines, metax c500 gpus, core cpu implementation, computationally efficient solution, complex workflow setups, around 48 h, enabled fep calculations, conducting fep calculations, energy perturbation calculations, energy perturbation, energy calculations, previous cpu, gpus free, around 1, energy community, widespread adoption, thereby paving, source project, promising tool, nvidia a100
Availability: https://doi.org/10.1021/acsomega.5c00151.s001
https://figshare.com/articles/journal_contribution/Acceleration_of_the_GROMACS_Free-Energy_Perturbation_Calculations_on_GPUs/29194550 -
19
Authors: et al.
Subject Terms: Biophysics, Cell Biology, Pharmacology, Cancer, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, vector using pyfeat, u >< b, point evaluation strategy, merging known interactions, https :// github, freely available tool, mediated cellular communication, intracellular communication networks, potential drug targets, interacting lrps mif, decoded cellular crosstalk, cellcdmt visualized intercellular, cellcdmt filters interactions, unlabeled lrp based, interpreting lri candidates, cell communication, lrps ), drug design, visualizes crosstalk, ular crosstalk, cellcdmt depicts, vital mediators, tfrc may, sigmoid plot
Relation: https://figshare.com/articles/journal_contribution/Prediction_of_Ligand_Receptor_Interactions_Based_on_CatBoost_and_Deep_Forest_and_Their_Application_in_Cell_Cell_Communication_Analysis/29196646
Availability: https://doi.org/10.1021/acs.jcim.5c00726.s001
https://figshare.com/articles/journal_contribution/Prediction_of_Ligand_Receptor_Interactions_Based_on_CatBoost_and_Deep_Forest_and_Their_Application_in_Cell_Cell_Communication_Analysis/29196646 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Computational Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, two end points, single initial round, rizzi et al, predicted mixing time, https :// github, free energy difference, based drug design, nonphysical thermodynamic pathway, discrete intermediates along, choose alchemical paths, simple toy model, free energy simulations, thermodynamic trailblazing algorithm, ee simulation based, alchemical intermediates, thermodynamic length, model selection, ee simulation, alchemical transformation, simple method, usually performed, several improvements
Relation: https://figshare.com/articles/journal_contribution/Simple_Method_to_Optimize_the_Spacing_and_Number_of_Alchemical_Intermediates_in_Expanded_Ensemble_Free_Energy_Calculations/29223861
Availability: https://doi.org/10.1021/acs.jcim.5c00704.s001
https://figshare.com/articles/journal_contribution/Simple_Method_to_Optimize_the_Spacing_and_Number_of_Alchemical_Intermediates_in_Expanded_Ensemble_Free_Energy_Calculations/29223861
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