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Enhancing encrypted HTTPS traffic classification based on stacked deep ensembles models

Authors: Ahmed M. Elshewey Ahmed M. Osman

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-22 (2025)

Subject Terms: HTTPS traffic classification, Encrypted traffic, Network security, Network traffic classification, Deep learning, Ensemble learning, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/cd8f8e99ded44ac2b23fc0de09acc54e

The HTTP Garden: Discovering Parsing Vulnerabilities in HTTP/1.1 Implementations by Differential Fuzzing of Request Streams

Authors: Kallus, Ben Anantharaman, Prashant Locasto, Michael et al.

Index Terms: Computer Science - Cryptography and Security, Computer Science - Networking and Internet Architecture, text

URL: http://arxiv.org/abs/2405.17737

DeepPSA: A Geometric Deep Learning Model for PROTAC Synthetic Accessibility Prediction

Authors: Ran Zhang Shihang Wang Lin Wang et al.

Subject Terms: Biochemistry, Genetics, Molecular Biology, Biotechnology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, target proteins via, molecules remain underdeveloped, https :// bailab, generative artificial intelligence, garnered significant attention, demonstrate superior performance, based partitioned datasets, based model built, https :// github, exceptional generalization ability, drug design due, experimental synthetic data, protac synthetic accessibility, synthetic accessibility, github repository, web server, test set, targeting chimeras, protac synthesis, prediction accuracy, novel compounds, house dataset, essential tool, driven approach

Relation: https://figshare.com/articles/journal_contribution/DeepPSA_A_Geometric_Deep_Learning_Model_for_PROTAC_Synthetic_Accessibility_Prediction/29403711

Availability: https://doi.org/10.1021/acs.jcim.5c00366.s001
https://figshare.com/articles/journal_contribution/DeepPSA_A_Geometric_Deep_Learning_Model_for_PROTAC_Synthetic_Accessibility_Prediction/29403711

DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology

Authors: Iverson Conrado Bezerra Jéssika de Oliveira Viana Karen Cacilda Weber 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

Supervised Contrastive Learning Leads to More Reasonable Spectral Embeddings

Authors: Peng Xiong Hongtao Xu Haoran Zheng

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

Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes

Authors: Andrea C. Graf Julian Libiseller-Egger Mathias Gotsmy 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

QUEST Database of Highly-Accurate Excitation Energies

Authors: Pierre-François Loos Martial Boggio-Pasqua Aymeric Blondel 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

Sicherstellung der Rückwärtskompatibilität von ASP.NET Core C# HTTP REST-APIs durch automatisierte technische Maßnahmen

Authors: Zauner, Daniel

Index Terms: ASP.NET Core, API, Breaking Changes, Statische Code-Analyse, MIT, Diplomarbeit (MA) JG20

Identification of Protein Cryptic Sites via Conformational Dynamics Capturing and Water-Based Pocket Characterization in Molecular Dynamics Simulations

Authors: Tianming Qu Steven L. Austin Lianqing Zheng 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

AbSet: A Standardized Data Set of Antibody Structures for Machine Learning Applications

Authors: Diego S. Almeida Matheus V. Almeida Jean V. Sampaio et al.

Subject Terms: Biophysics, Biochemistry, Biotechnology, Immunology, Cancer, Hematology, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, specific databases often, reference experimental complexes, provide molecular descriptors, machine learning applications, incorrect quality based, corresponding molecular descriptors, accompanying scripts hosted, protein data bank, publicly available via, generate structural variants, https :// github, curated dataset comprising, standardized data set, 000 antibody structures, data sets, structural similarity, decoy set, available structures, zenodo repository, therapeutic antibodies

Relation: https://figshare.com/articles/journal_contribution/AbSet_A_Standardized_Data_Set_of_Antibody_Structures_for_Machine_Learning_Applications/29031922

Availability: https://doi.org/10.1021/acs.jcim.5c00410.s002
https://figshare.com/articles/journal_contribution/AbSet_A_Standardized_Data_Set_of_Antibody_Structures_for_Machine_Learning_Applications/29031922

To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry

Authors: Naim Abdul-Khalek Mario Picciani Omar Shouman et al.

Subject Terms: Biochemistry, Sociology, Science Policy, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, specific experimental conditions, resulting physicochemical properties, ms data challenges, adaptability allows researchers, synthetic peptide library, peptide identification due, offering high performance, improving predictive capacity, https :// github, deep learning model, peptide detectability prediction, peptide detectability, detectability prediction, peptide sequences, peptide sequence, improving accuracy, high variability, subsequently fine, strongly related, species datasets, reliable state, protein abundance, outperforming state, negative impact, mass spectrometry

Relation: https://figshare.com/articles/journal_contribution/To_Fly_or_Not_to_Fly_That_Is_the_Question_A_Deep_Learning_Model_for_Peptide_Detectability_Prediction_in_Mass_Spectrometry/28996342

Availability: https://doi.org/10.1021/acs.jproteome.4c00973.s001
https://figshare.com/articles/journal_contribution/To_Fly_or_Not_to_Fly_That_Is_the_Question_A_Deep_Learning_Model_for_Peptide_Detectability_Prediction_in_Mass_Spectrometry/28996342

The Sequel of HTTP Headers - Advanced Security Capabilities

Authors: Michael Schneider orcid:0000-0003-0772- Marc Ruef

Contributors: Michael Schneider orcid:0000-0003-0772- Marc Ruef

Subject Terms: Ajax, Andrea Hauser, Basel, Browser, Firefox, GitHub, Google, Hardening, HTML, HTTP, Javascript, Master, Microsoft, Penetration Test, Policy, Report, Request, Research, Shop, Tool, Twitter, West

Relation: https://zenodo.org/records/3521919; oai:zenodo.org:3521919; https://doi.org/10.5281/zenodo.3521919

Availability: https://doi.org/10.5281/zenodo.3521919
https://zenodo.org/records/3521919

ComplexDnet: A Network-Based Strategy to Discover Critical Targets and Screen Active Compounds for Complex Diseases

Authors: Fei Pan Zhao-min Xu Ze-hui Liu 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

APEX: Automated Protein EXpression in Escherichia coli

Authors: Martyna Kasprzyk Michael A. Herrera Giovanni Stracquadanio

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

Design Space Exploration and Machine Learning Prediction of Hydrofluorocarbon Solubility in Ionic Liquids for Refrigerant Separation

Authors: Ashfaq Iftakher M. M. Faruque Hasan

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

Employing Artificial Neural Networks for Optimal Storage and Facile Sharing of Molecular Dynamics Simulation Trajectories

Authors: Abdul Wasim Lars V. Schäfer Jagannath Mondal

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

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results

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

Reverse Spectral Search Reimagined: A Simple but Overlooked Solution for Chimeric Spectral Annotation

Authors: Shipei Xing Vincent Charron-Lamoureux Haoqi Nina Zhao 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

AccFG: Accurate Functional Group Extraction and Molecular Structure Comparison

Authors: Xuan Liu Sarathkrishna Swaminathan Dmitry Zubarev 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

Allofusion: Allosteric Site Prediction Based on Language Models and Multi-Feature Fusion

Authors: Jiabin Huang Dongliang Guo Yapeng Liu et al.

Subject Terms: Biochemistry, Medicine, Pharmacology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, specific scoring matrices, localizing allosteric sites, identify allosteric sites, https :// github, evolutionary profiles derived, comprehensive results demonstrate, asd2023 data set, allosteric site prediction, 24 allosteric sites, modulating protein function, protein sequences, static structures, source code, promising strategy, promising method, modality features, language models, embedding representations, drug discovery, diverse features, crucial role, biochemical properties

Availability: https://doi.org/10.1021/acs.jcim.5c01033.s001
https://figshare.com/articles/journal_contribution/Allofusion_Allosteric_Site_Prediction_Based_on_Language_Models_and_Multi-Feature_Fusion/29802869