Enhancing Food Engineering Through Machine Learning in Analyzing Biomolecular Structures

Authors: Shoulek, Reem Ziad, Ibrahim, Sajjad Ghalib, Khishe, Mohammad, Saeed, Ali, Ghwanmeh, Sameh

Source: 2024 International Conference on Decision Aid Sciences and Applications (DASA) Decision Aid Sciences and Applications (DASA), 2024 International Conference on. :1-10 Dec, 2024

Relation: 2024 International Conference on Decision Aid Sciences and Applications (DASA)

Computational Drug Discovery of Herbal Phytoconstituents: Targeting Egfr for Hepatocellular Carcinoma

Authors: Thombare, Kirti, Ghotekar, Gauri, Walekar, Pallavi, Gaware, Mangesh, Bombale, Bhagyashree, Desai, Sharav

Source: 2023 4th International Conference on Computation, Automation and Knowledge Management (ICCAKM) Computation, Automation and Knowledge Management (ICCAKM), 2023 4th International Conference on. :1-6 Dec, 2023

Relation: 2023 4th International Conference on Computation, Automation and Knowledge Management (ICCAKM)

Waterless structures in the Protein Data Bank

Authors: Alexander Wlodawer, Zbigniew Dauter, Pawel Rubach, Wladek Minor, Joanna I. Loch, Dariusz Brzezinski, Miroslaw Gilski, Mariusz Jaskolski

Source: IUCrJ, Vol 11, Iss 6, Pp 966-976 (2024)

Subject Terms: protein hydration, structure-factor statistics, structure-quality statistics, modeling errors, electron density, protein data bank, pdb-redo, protein structure, x-ray crystallography, Crystallography, QD901-999

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Relation: https://journals.iucr.org/paper?S2052252524009928; https://doaj.org/toc/2052-2525

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Using deep-learning predictions reveals a large number of register errors in PDB depositions

Authors: Filomeno Sánchez Rodríguez, Adam J. Simpkin, Grzegorz Chojnowski, Ronan M. Keegan, Daniel J. Rigden

Source: IUCrJ, Vol 11, Iss 6, Pp 938-950 (2024)

Subject Terms: deep learning, register errors, protein data bank, structure validation, alphafold2, Crystallography, QD901-999

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Relation: https://journals.iucr.org/paper?S2052252524009114; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/5e6b06cec2dd4c3b99bbba3590a1c3f6

Shaking the β-Bulges

Authors: Craveur, P., Narwani, T.J., Srinivasan, N., Gelly, J., Rebehmed, J., de Brevern, A.G.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 19(1):14-18 Jan, 2022

Advances in Explainable Artificial Intelligence

Contributors: Gianini, Gabriele, Portier, Pierre-Edouard

Subject Terms: activation function, ReLU family, activation function test, psychological profiling, predictive modeling, behavioral data, explainable artificial intelligence, rule extraction, counterfactual explanations, fairness, bias, artificial intelligence, machine learning, psychiatry, health, mental health, federated learning, 6G, vehicle-to-everything (V2X), quality of service, quality of experience, interactive machine learning, decision tree classifiers, transparent-by-design, parallel coordinates, natural language generation, fact-checking, explainable AI, deep learning, LSTM, Arabic sentiment analysis, Explainable AI, text mining, random forest, multi-layer perceptron, protein data bank, neural network, artificial neural networks, knowledge representation, source code analysis, text classification, uncertainty quantification, efficiency, electroencephalography, convolutional variational autoencoder, latent space interpretation, spectral topographic maps, Computer science

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Access URL: https://directory.doabooks.org/handle/20.500.12854/137616
https://mdpi.com/books/pdfview/book/8803

Deepsharpen: Deep-Learning Based Sharpening Of 3D Reconstruction Map From Cryo-Electron Microscopy

Authors: Zehni, Mona, Do, Minh N., Zhao, Zhizhen

Source: 2020 IEEE 17th International Symposium on Biomedical Imaging Workshops (ISBI Workshops) Biomedical Imaging Workshops (ISBI Workshops), 2020 IEEE 17th International Symposium on. :1-4 Apr, 2020

Relation: 2020 IEEE 17th International Symposium on Biomedical Imaging Workshops (ISBI Workshops)

Review of the crystallized structures of the SARS-CoV-2 papain-like protease

Authors: Yue, Qiu ^{a, c, 1}, Hua-Juan, Jiang ^a, Yu-Shun, Yang ^a, Xiao-Qin, Hu ^{a, b, ⁎}, Xue-Wen, Zeng ^{a, ⁎}

Source: In Journal of Molecular Structure 25 June 2025 1333

Protein identification using Cryo-EM and artificial intelligence guides improved sample purification

Authors: Carr, Kenneth D. ^{a, b, 1}, Zambrano, Dane Evan D. ^{a, b, 1}, Weidle, Connor ^{a, b}, Goodson, Alex ^{a, b}, Eisenach, Helen E. ^{a, b}, Pyles, Harley ^{a, b}, Courbet, Alexis ^{a, b}, King, Neil P. ^{a, b}, Borst, Andrew J. ^{a, b, ⁎}

Source: In Journal of Structural Biology: X June 2025 11

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

Authors: Stephen K. Burley, Dennis W. Piehl, Brinda Vallat, Christine Zardecki

Source: IUCrJ, Vol 11, Iss 3, Pp 279-286 (2024)

Subject Terms: rcsb protein data bank, experimental structural biology, computed structure models, integrative structures, training, validation protocols, Crystallography, QD901-999

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Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252524002604; https://doaj.org/toc/2052-2525

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Biomolecular Data Science—in Honor of Professor Philip E. Bourne

Contributors: Mura, Cameron, Xie, Lei

Subject Terms: structure-based drug discovery, ligand binding sites, deep learning, graph neural network, CRISPR/Cas9, genome editing, machine learning, SHAP values, binding energy, off-targets, drug discovery, retrosynthesis, reaction template, recurrent neural network, and graph neural network, mutational signatures, smoking, lung cancers, APOBEC, immune response to smoking, cell-type composition, goblet cells, ciliated cells, basal cells, Protein Data Bank, Open Access, Worldwide Protein Data Bank, macromolecular crystallography, cryogenic electron microscopy, cryogenic electron tomography, electron crystallography, micro-electron diffraction, nuclear magnetic resonance spectroscopy, biological macromolecules, proteins, nucleic acids, DNA, RNA, carbohydrates, small-molecule ligands, social determinants of health, electronic health records, real-world evidence, census tract, data science, protein database, search tool, prioritization algorithm, drug repositioning, quantum machine learning, quantum metric learning, kernel method, kernel classifiers, structural bioinformatics, function annotation, specificity annotation, MSA, entropy, variability, amino acids, Philip Bourne, FAIR, bioinformatics, protein kinases, functional families, KinFams, KinBase classification, large language models, pharmacovigilance, social media, drugs of abuse, DNA sequencing, read classification, metagenomics, Research and information: general, Biology, life sciences

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Access URL: https://directory.doabooks.org/handle/20.500.12854/113952
https://mdpi.com/books/pdfview/book/7796

Community recommendations on cryoEM data archiving and validation

Authors: Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Catherine L. Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H. W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar

Source: IUCrJ, Vol 11, Iss 2, Pp 140-151 (2024)

Subject Terms: cryogenic-specimen electron microscopy, data archiving, validation, quality control, electron microscopy data bank, protein data bank, single-particle cryoem, databases, bioinformatics, structure determination, Crystallography, QD901-999

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Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252524001246; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/0e43f020fe4a4894b6f5aa6a5fd3dc2f

Identifications of False Positives Amongst Sodium(I) Cations in Protein Three-Dimensional Structures—A Validation Approach Extendible to Any Alkali or Alkaline Earth Cation and to Any Monoatomic Anion

Authors: Oliviero Carugo

Source: Crystals, Vol 14, Iss 11, p 918 (2024)

Subject Terms: alkali, alkaline earth, monoatomic anion, metal, Protein Data Bank, sodium, Crystallography, QD901-999

File Description: electronic resource

Relation: https://www.mdpi.com/2073-4352/14/11/918; https://doaj.org/toc/2073-4352

Access URL: https://doaj.org/article/bae4cf36dffd4306b35a2b6683922656

Unveiling the Druggable Landscape of Bacterial Peptidyl tRNA Hydrolase: Insights into Structure, Function, and Therapeutic Potential

Authors: Surbhi Mundra, Ashish Kabra

Source: Biomolecules, Vol 14, Iss 6, p 668 (2024)

Subject Terms: peptidyl-tRNA hydrolase, protein structure, Protein Data Bank, X-ray crystallography, NMR spectroscopy, esterase, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/2218-273X/14/6/668; https://doaj.org/toc/2218-273X

Access URL: https://doaj.org/article/fea32a6bbb214f168880ebd6d0512ea1

Non-covalent Interactions in Coordination and Organometallic Chemistry

Contributors: Novikov, Alexander S.

Subject Terms: non-covalent interactions, crystal engineering, organometallic compounds, coordination compounds, crystalline materials, supramolecular systems, hydrazones, sonochemical-based synthesis, single-crystal analysis, non-covalent interaction, Hirshfeld surface study, silver phosphine, pyrazole, luminescence, TD-DFT, IsoStar, Cambridge Structural Database, Protein Data Bank, noncovalent interactions, crystal structure, coordination polymer, sonochemical route, X-ray crystallography, nanorods, Pb(II), ultrasonic irradiation, nano metal oxide, Technology: general issues

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Access URL: https://directory.doabooks.org/handle/20.500.12854/79617
https://mdpi.com/books/pdfview/book/5002

Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank.

Authors: Warr, Wendy A.¹ wendy@warr.com

Source: Journal of Computer-Aided Molecular Design. Oct2008, Vol. 22 Issue 10, p707-710. 4p.

Subject Terms: *BIOINFORMATICS, *INFORMATION science

Geographic Terms: UNITED States

Company/Entity: WORLDWIDE Protein Data Bank (Organization)

People: BERMAN, Helen

AS THE PROTEIN DATA BANK THRIVES, ITS FUNDING IS RENEWED AT INCREASED LEVELS

Source: States News Service. January 14, 2025

Protein Secondary Structure Prediction Using Support Vector Machines (SVMs)

Authors: Patel, M., Shah, H.

Source: 2013 International Conference on Machine Intelligence and Research Advancement Machine Intelligence and Research Advancement (ICMIRA), 2013 International Conference on. :594-598 Dec, 2013

Relation: 2013 International Conference on Machine Intelligence and Research Advancement (ICMIRA)

PROTEIN FOLDS IN THE ALL-{beta} AND ALL-{alpha} CLASSES.

Authors: Chothia, Cyrus, Hubbard, Tim, Brenner, Steven, Barns, Hugh, Murzin, Alexey

Source: Annual Review of Biophysics & Biomolecular Structure. 1997, Vol. 26 Issue 1, p597. 31p. 13 Black and White Photographs, 2 Diagrams, 1 Graph.

Subject Terms: *PROTEINS

Company/Entity: WORLDWIDE Protein Data Bank (Organization)

A software tool for extraction of annotation data from a PDB file

Authors: Mandal, Amit Kr., Indra Gopal Das, Bhattacharjee, Debotosh

Source: 2012 3rd National Conference on Emerging Trends and Applications in Computer Science Emerging Trends and Applications in Computer Science (NCETACS), 2012 3rd National Conference on. :31-37 Mar, 2012

Relation: 2012 3rd National Conference on Emerging Trends and Applications in Computer Science (NCETACS)