Search Results - "Databases, Protein"

Storing Mass-Spectrometry Data in Simple Databases Enables Flexible and Intuitive Exploration without Time or Space Penalties.

Authors: Kumler W LaRue S Ingalls AE

Source: Journal of proteome research [J Proteome Res] 2025 Dec 05; Vol. 24 (12), pp. 6174-6185. Date of Electronic Publication: 2025 Nov 24.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

MeSH Terms: Mass Spectrometry*/methods , Information Storage and Retrieval*/methods , Databases, Protein* , Databases, Factual*, Software

Identification of engineered IMGT Fc variants in IMGT/mAb-DB, a database of therapeutic antibodies and fusion proteins.

Authors: Manso T Sanou G Nousias C et al.

Source: MAbs [MAbs] 2025 Dec; Vol. 17 (1), pp. 2594260. Date of Electronic Publication: 2025 Nov 27.

Publication Type: Journal Article

Journal Info: Publisher: Taylor & Francis Country of Publication: United States NLM ID: 101479829 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1942-0870 (Electronic) Linking ISSN: 19420862 NLM ISO Abbreviation: MAbs Subsets: MEDLINE

MeSH Terms: Antibodies, Monoclonal*/genetics , Antibodies, Monoclonal*/therapeutic use , Antibodies, Monoclonal*/chemistry , Antibodies, Monoclonal*/immunology , Immunoglobulin Fc Fragments*/genetics , Immunoglobulin Fc Fragments*/immunology , Immunoglobulin Fc Fragments*/chemistry , Protein Engineering*/methods , Recombinant Fusion Proteins*/genetics , Recombinant Fusion Proteins*/chemistry , Recombinant Fusion Proteins*/therapeutic use , Recombinant Fusion Proteins*/immunology , Databases, Protein*, Humans

PDB-CAT: A user-friendly tool to classify and analyze PDB protein-ligand complexes.

Authors: Llop-Peiró A Trujillo-De León S Pujadas G et al.

Source: Protein science : a publication of the Protein Society [Protein Sci] 2025 Dec; Vol. 34 (12), pp. e70379.

Publication Type: Journal Article

Journal Info: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Software* , SARS-CoV-2*/chemistry , SARS-CoV-2*/enzymology , Proteins*/chemistry , Proteins*/metabolism, Ligands ; Protein Binding ; Humans ; Protein Conformation

SAAINT-DB: a comprehensive structural antibody database for antibody modeling and design.

Authors: Huang X Zhou J Chen S et al.

Source: Acta pharmacologica Sinica [Acta Pharmacol Sin] 2025 Dec; Vol. 46 (12), pp. 3365-3375. Date of Electronic Publication: 2025 Jun 30.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: United States NLM ID: 100956087 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1745-7254 (Electronic) Linking ISSN: 16714083 NLM ISO Abbreviation: Acta Pharmacol Sin Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Antibodies*/chemistry , Antibodies*/immunology , Drug Design*, Humans ; Models, Molecular

Using protein blocks to build custom fragment libraries from protein structures.

Authors: Dhingra S Téletchéa S Sowdhamini R et al.

Source: Biochimie [Biochimie] 2025 Dec; Vol. 239 (Pt B), pp. 72-81. Date of Electronic Publication: 2025 Aug 13.

Publication Type: Journal Article

Journal Info: Publisher: Editions Scientifiques Elsevier Country of Publication: France NLM ID: 1264604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1638-6183 (Electronic) Linking ISSN: 03009084 NLM ISO Abbreviation: Biochimie Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Proteins*/chemistry , Peptide Library*, Protein Conformation

ricePSP: a database of rice phase separation-associated proteins.

Authors: Gao R Guo M Luan S et al.

Source: Genome biology [Genome Biol] 2025 Nov 17; Vol. 26 (1), pp. 390. Date of Electronic Publication: 2025 Nov 17.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE

MeSH Terms: Oryza*/genetics , Oryza*/metabolism , Plant Proteins*/chemistry , Plant Proteins*/metabolism , Plant Proteins*/genetics , Databases, Protein*, Flowers/genetics ; Intrinsically Disordered Proteins/chemistry ; Phase Separation

BrainProt v3.0: An Integrative and Simplified Omics-Based Knowledge-Base About the Human Brain and Its Associated Diseases.

Authors: Biswas D Shenoy SV Chauhan A et al.

Source: Journal of proteome research [J Proteome Res] 2025 Nov 07; Vol. 24 (11), pp. 5352-5369. Date of Electronic Publication: 2025 Sep 26.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE

MeSH Terms: Brain*/metabolism , Brain*/pathology , Knowledge Bases* , Brain Diseases*/genetics , Brain Diseases*/metabolism , Proteomics*/methods , Proteome*/genetics , Proteome*/metabolism , Databases, Protein*, Humans ; Transcriptome

Proteoform search from protein database with top-down mass spectra.

Authors: Li K Shan B Xin L et al.

Source: Nature computational science [Nat Comput Sci] 2025 Nov; Vol. 5 (11), pp. 998-1009. Date of Electronic Publication: 2025 Oct 03.

Publication Type: Journal Article

Journal Info: Publisher: Springer Nature Country of Publication: United States NLM ID: 101775476 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2662-8457 (Electronic) Linking ISSN: 26628457 NLM ISO Abbreviation: Nat Comput Sci Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Proteins*/chemistry , Mass Spectrometry*/methods , Proteomics*/methods, Algorithms ; Computational Biology/methods

Glycoprotein-Notebook: A Pan-Cancer Glycoproteomic Database and Toolkit for Analysis of Protein Glycosylation Changes Associated With Cancer Phenotypes.

Authors: Zhang H Hoang T Hu Y

Source: Molecular & cellular proteomics : MCP [Mol Cell Proteomics] 2025 Nov; Vol. 24 (11), pp. 101089. Date of Electronic Publication: 2025 Oct 13.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Inc. on behalf of American Society for Biochemistry and Molecular Biology Country of Publication: United States NLM ID: 101125647 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-9484 (Electronic) Linking ISSN: 15359476 NLM ISO Abbreviation: Mol Cell Proteomics Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Glycoproteins*/metabolism , Databases, Protein* , Neoplasms*/metabolism , Pancreatic Neoplasms*/metabolism, Glycosylation ; Humans ; Phenotype ; Glycopeptides/metabolism ; Carcinoma, Pancreatic Ductal/metabolism

Viro3D: a comprehensive database of virus protein structure predictions.

Authors: Litvin U Lytras S Jack A et al.

Source: Molecular systems biology [Mol Syst Biol] 2025 Nov; Vol. 21 (11), pp. 1599-1617. Date of Electronic Publication: 2025 Sep 16.

Publication Type: Journal Article

Journal Info: Publisher: EMBO Press Country of Publication: Germany NLM ID: 101235389 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1744-4292 (Electronic) Linking ISSN: 17444292 NLM ISO Abbreviation: Mol Syst Biol Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Viral Proteins*/chemistry , Viral Proteins*/genetics , Viruses*/chemistry , Viruses*/genetics, Humans ; Protein Conformation ; Animals ; Evolution, Molecular ; Phylogeny

Ten rules for a structural bioinformatic analysis.

Authors: Wankowicz SA; Departments of Molecular Physiology and Biophysics, Biochemistry, Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America.; Center for Applied AI in Protein Dynamics, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Oct 31; Vol. 21 (10), pp. e1013094. Date of Electronic Publication: 2025 Oct 31 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Databases, Protein* , Proteins*/chemistry , Proteins*/ultrastructure, Protein Conformation ; Models, Molecular

Comparison of Molecular Recognition in Docking Versus Experimental CSD and PDB Data.

Authors: Tosstorff A Kuhn B

Source: Journal of chemical information and modeling [J Chem Inf Model] 2025 Oct 13; Vol. 65 (19), pp. 10390-10399. Date of Electronic Publication: 2025 Jul 14.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

MeSH Terms: Molecular Docking Simulation* , Databases, Protein* , Proteins*/chemistry , Proteins*/metabolism, Ligands ; Algorithms ; Protein Conformation

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.

Authors: Odai R Leemann M Al-Murad T et al.

Source: Science advances [Sci Adv] 2025 Oct 03; Vol. 11 (40), pp. eadz8560. Date of Electronic Publication: 2025 Oct 01.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 101653440 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2375-2548 (Electronic) Linking ISSN: 23752548 NLM ISO Abbreviation: Sci Adv Subsets: MEDLINE

MeSH Terms: Archaea*/virology , Bacteria*/virology , Protein Folding* , Eukaryota*/virology , Viruses*/chemistry , Viruses*/metabolism , Viruses*/genetics , Databases, Protein* , Viral Proteins*/chemistry , Viral Proteins*/metabolism , Viral Proteins*/genetics , Protein Multimerization*, Models, Molecular

BAV-LLPS: a database of bacterial, archaea, and virus liquid-liquid phase separation proteins.

Authors: Rodriguez CB Tunque Cahui RR Demitroff N et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Oct 02; Vol. 41 (10).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Archaea*/metabolism , Viral Proteins*/chemistry , Archaeal Proteins*/chemistry , Bacterial Proteins*/chemistry, Viruses/chemistry ; Bacteria ; Phase Separation

Databases and web-based tools for studying structures of protein-nucleic acid complexes.

Authors: Dapkūnas J Venclovas Č

Source: Current opinion in structural biology [Curr Opin Struct Biol] 2025 Oct; Vol. 94, pp. 103079. Date of Electronic Publication: 2025 Jun 11.

Publication Type: Journal Article; Review

Journal Info: Publisher: Elsevier Science Country of Publication: England NLM ID: 9107784 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-033X (Electronic) Linking ISSN: 0959440X NLM ISO Abbreviation: Curr Opin Struct Biol Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Internet* , Proteins*/chemistry , Proteins*/metabolism , Nucleic Acids*/chemistry , Nucleic Acids*/metabolism , Computational Biology*/methods, Models, Molecular ; Protein Conformation ; Protein Binding

Validation of helical symmetry parameters in the EMDB.

Authors: Li D Muñoz Pérez M Zhang X et al.

Source: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2025 Oct 01; Vol. 81 (Pt 10), pp. 527-534. Date of Electronic Publication: 2025 Sep 04.

Publication Type: Journal Article; Validation Study

Journal Info: Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101676043 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2059-7983 (Electronic) Linking ISSN: 20597983 NLM ISO Abbreviation: Acta Crystallogr D Struct Biol Subsets: MEDLINE

MeSH Terms: Cryoelectron Microscopy*/methods , Databases, Protein* , Amyloid*/chemistry, Models, Molecular

MRMAssayDB: a comprehensive integrated resource for targeted proteomics assays.

Authors: Mohammed Y Bhowmick P Borchers CH

Source: Expert review of proteomics [Expert Rev Proteomics] 2025 Oct; Vol. 22 (10), pp. 421-432. Date of Electronic Publication: 2025 Sep 18.

Publication Type: Journal Article; Review

Journal Info: Publisher: Informa Healthcare Country of Publication: England NLM ID: 101223548 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1744-8387 (Electronic) Linking ISSN: 14789450 NLM ISO Abbreviation: Expert Rev Proteomics Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Databases, Protein*, Humans ; Protein Processing, Post-Translational

Case Studies of Orphan Domain Reclassification in ECOD by Expert Curation.

Authors: Pei J Schaeffer RD Cong Q et al.

Source: Proteins [Proteins] 2025 Oct; Vol. 93 (10), pp. 1780-1789. Date of Electronic Publication: 2025 May 26.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Proteins*/chemistry , Proteins*/classification , Proteins*/genetics , Protein Domains*, Evolution, Molecular ; Models, Molecular ; Humans ; Computational Biology/methods

Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.

Authors: Rajczewski AT Mehta S Wagner R et al.

Source: Journal of proteomics [J Proteomics] 2026 Jan 06; Vol. 322, pp. 105549. Date of Electronic Publication: 2025 Oct 21.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101475056 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1876-7737 (Electronic) Linking ISSN: 18743919 NLM ISO Abbreviation: J Proteomics Subsets: MEDLINE

MeSH Terms: Proteomics*/methods , Microbiota* , Databases, Protein* , Search Engine*/methods, Tandem Mass Spectrometry ; Bacterial Proteins/analysis

Vanalyzer: an open-source tool for automated statistical analysis and continuous updating of vanadate-binding sites in the Protein Data Bank.

Authors: Trachtenberg A Akabayov B

Source: Journal of molecular graphics & modelling [J Mol Graph Model] 2026 Jan; Vol. 142, pp. 109223. Date of Electronic Publication: 2025 Nov 17.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Science, Inc Country of Publication: United States NLM ID: 9716237 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4243 (Electronic) Linking ISSN: 10933263 NLM ISO Abbreviation: J Mol Graph Model Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Vanadates*/chemistry , Vanadates*/metabolism , Software* , Proteins*/chemistry, Binding Sites ; Protein Binding ; Models, Molecular