Search Results - computational tools and databases

Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis

Authors: Tanzeel Bashir Amjad M. Husaini

Source: Functional & Integrative Genomics. 25

Subject Terms: Crops, Agricultural, MicroRNAs, RNA, Untranslated, Gene Expression Regulation, Plant, RNA, Plant, Databases, Genetic, Computational Biology, RNA, Long Noncoding, Algorithms

Access URL: https://pubmed.ncbi.nlm.nih.gov/40183947

Computational Thinking beyond Coding: Exploring Student Computational Practices While Playing and Modifying a Socio-Scientific Simulation Game with Integrated Computational Tools

Authors: Marianthi Grizioti (ORCID 0000-0001-9670-0359)

Source: Educational Technology Research and Development. 2025 73(4):2251-2278.

Peer Reviewed: Y

Page Count: 28

Descriptors: Computation, Thinking Skills, Coding, Play, Educational Games, Science and Society, Simulation, Computer Science Education, Programming, Databases, Problem Solving, Middle School Students, Cooperative Learning, Affordances, Design, Game Based Learning, Systems Approach

Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering

Authors: Md. Mojnu Mia Habiba Sultana Md. Al Amin et al.

Source: Engineering Reports, Vol 7, Iss 2, Pp n/a-n/a (2025)

Subject Terms: protein computational resources, protein design, protein engineering, protein engineering tools, Engineering (General). Civil engineering (General), TA1-2040, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://doaj.org/toc/2577-8196

Access URL: https://doaj.org/article/39bf1038e52c4a5790fe2b2cdc47761b

Current status of antimicrobial peptides databases and computational tools for optimization

Authors: Madhulika Jha Akash Nautiyal Kumud Pant et al.

Source: Environment Conservation Journal, Vol 26, Iss 1 (2025)

Subject Terms: AFPs, AMPs, Antifungal peptide, Candida albicans, Candida glabrata, Environmental sciences, GE1-350

File Description: electronic resource

Relation: https://journal.environcj.in/index.php/ecj/article/view/2932; https://doaj.org/toc/0972-3099; https://doaj.org/toc/2278-5124

Access URL: https://doaj.org/article/3ce2de75da6d40ef9e1fc6aae0e2166d

Unlocking the potential of CRISPR tools and databases for precision genome editing

Authors: Pooja Saraswat Rajiv Ranjan

Source: Frontiers in Plant Science, Vol 16 (2025)

Subject Terms: CRISPR/Cas, genome editing, computational tools, databases, guide RNA design, off target prediction, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpls.2025.1563711/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/e1db9212e3904c27914b8fe5f2dd9e34

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools.

Authors: He S Zhang F

Source: Journal of visualized experiments : JoVE [J Vis Exp] 2025 Aug 19 (222). Date of Electronic Publication: 2025 Aug 19.

Publication Type: Journal Article; Video-Audio Media

Journal Info: Publisher: MYJoVE Corporation Country of Publication: United States NLM ID: 101313252 Publication Model: Electronic Cited Medium: Internet ISSN: 1940-087X (Electronic) Linking ISSN: 1940087X NLM ISO Abbreviation: J Vis Exp Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Mass Spectrometry*/methods , Software* , Computational Biology*/methods, Databases, Protein

Meta-EA: a gene-specific combination of available computational tools for predicting missense variant effects.

Authors: Katsonis P Lichtarge O

Source: Nature communications [Nat Commun] 2025 Jan 02; Vol. 16 (1), pp. 159. Date of Electronic Publication: 2025 Jan 02.

Publication Type: Journal Article; Research Support, U.S. Gov't, P.H.S.; Research Support, N.I.H., Extramural

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Mutation, Missense* , Computational Biology*/methods, Humans ; Gene Frequency ; ROC Curve ; Polymorphism, Single Nucleotide ; Databases, Genetic ; Software

Making fundamental scientific discoveries by combining information from literature, databases, and computational tools – An example

Authors: Bastian Stielow Clara Simon Robert Liefke

Source: Computational and Structural Biotechnology Journal, Vol 19, Iss , Pp 3027-3033 (2021)

Subject Terms: Databases, Protein structure prediction, SAMD1, CpG islands, Transcription factors, Human genome, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037021001641; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/95fe3ba7b64d49a288abcc62bdb92acc

Current computational tools for protein lysine acylation site prediction.

Authors: Qin Z Ren H Zhao P et al.

Source: Briefings in bioinformatics [Brief Bioinform] 2024 Sep 23; Vol. 25 (6).

Publication Type: Journal Article; Systematic Review

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Lysine*/metabolism , Lysine*/chemistry , Protein Processing, Post-Translational* , Proteins*/metabolism , Proteins*/chemistry, Humans ; Acylation ; Algorithms ; Databases, Protein ; Software

Cancer pharmacoinformatics: Databases and analytical tools.

Authors: Kamble P Nagar PR Bhakhar KA et al.

Source: Functional & integrative genomics [Funct Integr Genomics] 2024 Sep 19; Vol. 24 (5), pp. 166. Date of Electronic Publication: 2024 Sep 19.

Publication Type: Journal Article; Review

Journal Info: Publisher: Springer Country of Publication: Germany NLM ID: 100939343 Publication Model: Electronic Cited Medium: Internet ISSN: 1438-7948 (Electronic) Linking ISSN: 1438793X NLM ISO Abbreviation: Funct Integr Genomics Subsets: MEDLINE

MeSH Terms: Neoplasms*/drug therapy , Neoplasms*/genetics , Drug Discovery*, Humans ; Computational Biology/methods ; Antineoplastic Agents/therapeutic use ; Databases, Factual ; Software ; Machine Learning

Understanding the physical origin, topology and strength of noncovalent interactions by means of computational tools

Authors: Velasquez Benites, Juan Diego

Contributors: University/Department: Universitat de Barcelona. Departament de Química Inorgànica i Orgànica

Thesis Advisors: Álvarez, Santiago (Álvarez Reverter), Echeverria Lopez, Jorge

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Química orgànica, Química orgánica, Organic chemistry, Enllaços químics, Enlaces químicos, Chemical bonds, Estructura electrònica, Estructura electrónica, Electronic structure, Compostos organometàl·lics, Compuestos organometálicos, Organometallic compounds, Ciències Experimentals i Matemàtiques

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/674956

Examining the specification of gamma-ray shielding with increasing TiO2 concentration in the Bi2O3-ZnO-Pb3O4-Al2O3 glass sample with simulation and computational tools

Authors: A. Arvaneh A. Asadi S.A. Hosseini

Source: مجله علوم و فنون هسته‌ای, Vol 44, Iss 4, Pp 76-84 (2023)

Subject Terms: gamma-ray, buildup factor, mcnp code and the xcom database, attenuation parameters shielding materials, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798

File Description: electronic resource

Relation: https://jonsat.nstri.ir/article_1529_52cbf3eac60637a1ec6f3a454eb9c4cd.pdf; https://doaj.org/toc/1735-1871; https://doaj.org/toc/2676-5861

Access URL: https://doaj.org/article/8b29e9c31bcf45909b5337eec277d978

Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.

Authors: Zhang 张天缘 T Jiang 蒋冕 M Li 李汉洲 H et al.

Source: Genomics, proteomics & bioinformatics [Genomics Proteomics Bioinformatics] 2025 Sep 22; Vol. 23 (4).

Publication Type: Journal Article; Review

Journal Info: Publisher: Oxford University Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation and Genetics Society of China Country of Publication: England NLM ID: 101197608 Publication Model: Print Cited Medium: Internet ISSN: 2210-3244 (Electronic) Linking ISSN: 16720229 NLM ISO Abbreviation: Genomics Proteomics Bioinformatics Subsets: MEDLINE

MeSH Terms: Metagenomics*/methods , High-Throughput Nucleotide Sequencing*/methods , Nanopores* , Software* , Nanopore Sequencing*/methods , Computational Biology*/methods, Metagenome ; Sequence Analysis, DNA/methods

Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins.

Authors: Kurgan L Hu G Wang K et al.

Source: Nature protocols [Nat Protoc] 2023 Nov; Vol. 18 (11), pp. 3157-3172. Date of Electronic Publication: 2023 Sep 22.

Publication Type: Journal Article; Review; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Intrinsically Disordered Proteins*/chemistry, Databases, Protein ; Amino Acid Sequence

Deep learning in the discovery of antiviral peptides and peptidomimetics: databases and prediction tools.

Authors: Nawaz M Huiyuan Y Akhtar F et al.

Source: Molecular diversity [Mol Divers] 2025 Aug; Vol. 29 (4), pp. 3753-3788. Date of Electronic Publication: 2025 Mar 28.

Publication Type: Journal Article; Review

Journal Info: Publisher: ESCOM Science Publishers Country of Publication: Netherlands NLM ID: 9516534 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-501X (Electronic) Linking ISSN: 13811991 NLM ISO Abbreviation: Mol Divers Subsets: MEDLINE

MeSH Terms: Peptidomimetics*/chemistry , Peptidomimetics*/pharmacology , Peptidomimetics*/therapeutic use , Deep Learning* , Antiviral Agents*/pharmacology , Antiviral Agents*/chemistry , Antiviral Agents*/therapeutic use , Peptides*/chemistry , Peptides*/pharmacology , Peptides*/therapeutic use , Drug Discovery*/methods, Humans ; SARS-CoV-2/drug effects ; Animals ; Databases, Factual ; COVID-19

A Practical Guide on Computational Tools and Databases for Transposable Elements in Plants.

Authors: Oliveira LS de Amorim TS Pedro DLF et al.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2250, pp. 31-53.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: DNA Transposable Elements*, Computational Biology/*methods , Plants/*genetics, Big Data ; DNA, Plant/genetics ; Data Mining ; Databases, Genetic

Challenges and recommendations to improve the installability and archival stability of omics computational tools.

Authors: Mangul, Serghei Mosqueiro, Thiago Abdill, Richard et al.

Source: PLoS Biology. 17(6)

Subject Terms: Biomedical Research, Computational Biology, Databases, Factual, Humans, Information Dissemination, Information Storage and Retrieval, Internet, Software

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/2144j4bv
https://escholarship.org/content/qt2144j4bv/qt2144j4bv.pdf

Computational tools to facilitate early warning of new emerging risk chemicals

Authors: Tariq, Farina Ahrens, Lutz Alygizakis, Nikiforos A. et al.

Source: Toxics. 12(10)

Subject Terms: artificial intelligence (AI), computational toxicology, early warning system (EWS), effect assessment, exposure assessment, new and emerging risk chemicals (NERCs), QSAR, risk assessment

File Description: electronic

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-231528
https://doi.org/10.3390/toxics12100736

Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.

Authors: Shad M Liaqat A Nazir A et al.

Source: Applied biochemistry and biotechnology [Appl Biochem Biotechnol] 2025 Nov; Vol. 197 (11), pp. 7015-7043. Date of Electronic Publication: 2025 Sep 09.

Publication Type: Journal Article; Review

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 8208561 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1559-0291 (Electronic) Linking ISSN: 02732289 NLM ISO Abbreviation: Appl Biochem Biotechnol Subsets: MEDLINE

MeSH Terms: Recombinant Proteins*/chemistry , Recombinant Proteins*/genetics , Recombinant Proteins*/metabolism , Computational Biology*/methods, Molecular Dynamics Simulation ; Software ; Molecular Docking Simulation

Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine.

Authors: Shawan MMAK Sharma AR Halder SK et al.

Source: International journal of peptide research and therapeutics [Int J Pept Res Ther] 2023; Vol. 29 (4), pp. 60. Date of Electronic Publication: 2023 May 23.

Publication Type: Journal Article; Review

Journal Info: Publisher: Springer Country of Publication: United States NLM ID: 101252761 Publication Model: Print-Electronic Cited Medium: Print ISSN: 1573-3149 (Print) Linking ISSN: 15733149 NLM ISO Abbreviation: Int J Pept Res Ther Subsets: PubMed not MEDLINE