Works about PROTEIN models

Results: 1198

ProtMamba: a homology-aware but alignment-free protein state space model Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf348

By:

Sgarbossa, Damiano;
Malbranke, Cyril;
Bitbol, Anne-Florence

Publication type:

Article

Pool PaRTI: a PageRank-based pooling method for identifying critical residues and enhancing protein sequence representations Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf330

By:

Tartici, Alp;
Nayar, Gowri;
Altman, Russ B

Publication type:

Article

DeepAllo: allosteric site prediction using protein language model (pLM) with multitask learning Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf294

By:

Khokhar, Moaaz;
Keskin, Ozlem;
Gursoy, Attila

Publication type:

Article

Mapping the space of protein binding sites with sequence-based protein language models Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf284

By:

Oruç, Tuğçe;
Kadukova, Maria;
Davies, Thomas G;
Verdonk, Marcel;
Poelking, Carl

Publication type:

Article

RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60872-5

By:

Penić, Rafael Josip;
Vlašić, Tin;
Huber, Roland G.;
Wan, Yue;
Šikić, Mile

Publication type:

Article

Charting γ-secretase substrates by explainable AI.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60638-z

By:

Breimann, Stephan;
Kamp, Frits;
Basset, Gabriele;
Abou-Ajram, Claudia;
Güner, Gökhan;
Yanagida, Kanta;
Okochi, Masayasu;
Müller, Stephan A.;
Lichtenthaler, Stefan F.;
Langosch, Dieter;
Frishman, Dmitrij;
Steiner, Harald

Publication type:

Article

Evolving fitness and immune escape: a retrospective analysis of SARS-CoV-2 spike protein (2020-2024) using protein language model.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1576414

By:

Peng, Sihua;
Lyu, Leke;
Carmola, Ludy Registre;
Subedi, Sachin;
Mubassir, M. H. M.;
Bakheet, Mohamed A.;
Bahl, Justin

Publication type:

Article

Structural insights into allosteric inhibition of HRI kinase by heme binding via HDX-MS.

Published in:

Biochemical Journal, 2025, v. 482, n. 12, p. 859, doi. 10.1042/BCJ20253072

By:

Kanta, Shivani;
Vinciauskaite, Vanesa;
Neill, Graham;
Muqit, Miratul M. K.;
Masson, Glenn R.

Publication type:

Article

Microfluidic Templating and Initiator‐Free Photocrosslinking of Protein‐Loaded PCL Microcapsules.

Published in:

Particle & Particle Systems Characterization, 2024, v. 41, n. 5, p. 1, doi. 10.1002/ppsc.202300099

By:

Störmann, Florian;
Roch, Toralf;
Lendlein, Andreas;
Wischke, Christian

Publication type:

Article

Comparison of separation modes for microchip electrophoresis of proteins.

Published in:

Journal of Separation Science, 2021, v. 44, n. 3, p. 744, doi. 10.1002/jssc.202000883

By:

Samarasinghe, Thushara N.;
Zeng, Yong;
Johnson, Carey K.

Publication type:

Article

Automatically obtaining a cellular automaton scheme for modeling protein folding using the FCC model.

Published in:

Natural Computing, 2019, v. 18, n. 2, p. 275, doi. 10.1007/s11047-018-9705-y

By:

Varela, Daniel;
Santos, José

Publication type:

Article

Anti-inflammatory potential of baicalein combined with silk fibroin protein in a zebrafish model (Danio rerio).

Published in:

Biotechnology Letters, 2023, v. 45, n. 2, p. 235, doi. 10.1007/s10529-022-03334-y

By:

Holanda, Fabrício H.;
Ribeiro, Arlefe N.;
Sánchez-Ortiz, Brenda L.;
de Souza, Gisele C.;
Borges, Swanny F.;
Ferreira, Adriana M.;
Florentino, Alexandro C.;
Yoshioka, Sérgio A.;
Moraes, Lienne S.;
Carvalho, José Carlos T.;
Ferreira, Irlon M.

Publication type:

Article

A novel method for the in vitro assembly of virus-like particles and multimeric proteins.

Published in:

Biotechnology Letters, 2021, v. 43, n. 6, p. 1155, doi. 10.1007/s10529-021-03093-2

By:

Rodríguez, Mabel;
Castro-Acosta, Ricardo M.;
Ruiz-Morales, Elias R.;
Villanueva-Flores, Francisca;
Ramírez, Octavio T.;
Palomares, Laura A.

Publication type:

Article

Small design from big alignment: engineering proteins with multiple sequence alignment as the starting point.

Published in:

Biotechnology Letters, 2020, v. 42, n. 8, p. 1305, doi. 10.1007/s10529-020-02914-0

By:

Wang, Tianwen;
Liang, Chen;
Hou, Yajing;
Zheng, Mengyuan;
Xu, Hongju;
An, Yafei;
Xiao, Sa;
Liu, Lu;
Lian, Shuaibin

Publication type:

Article

Feasible development of stable HEK293 clones by CRISPR/Cas9-mediated site-specific integration for biopharmaceuticals production.

Published in:

Biotechnology Letters, 2019, v. 41, n. 8/9, p. 941, doi. 10.1007/s10529-019-02702-5

By:

Yang, Hui;
Wang, Jiaxian;
Zhao, Menglin;
Zhu, Jianwei;
Zhang, Mengxiao;
Wang, Ziyan;
Gao, Yang;
Zhu, Wen;
Lu, Huili

Publication type:

Article

Organ and cell-specific biomarkers of Long-COVID identified with targeted proteomics and machine learning.

Published in:

Molecular Medicine, 2023, v. 29, n. 1, p. 1, doi. 10.1186/s10020-023-00610-z

By:

Patel, Maitray A.;
Knauer, Michael J.;
Nicholson, Michael;
Daley, Mark;
Van Nynatten, Logan R.;
Cepinskas, Gediminas;
Fraser, Douglas D.

Publication type:

Article

DPP4 inhibitor reinforces cell junction proteins in mouse model of short bowel syndrome.

Published in:

Pediatric Surgery International, 2020, v. 36, n. 1, p. 49, doi. 10.1007/s00383-019-04571-5

By:

Sueyoshi, Ryo;
Miyahara, Katsumi;
Nakazawa-Tanaka, Nana;
Fujiwara, Naho;
Ochi, Takanori;
Yamataka, Atsuyuki

Publication type:

Article

The Roots of Bio‐Molecular Simulation: The Eight‐Week CECAM Workshop 'Models for Protein Dynamics' of 1976.

Published in:

Helvetica Chimica Acta, 2019, v. 102, n. 8, p. N.PAG, doi. 10.1002/hlca.201800239

By:

van Gunsteren, Wilfred F.

Publication type:

Article

Expansion and Additional Validation of PKA17: A Fast Real-Time and Web-Based pKa Predictor.

Published in:

Journal of Computational Biophysics & Chemistry, 2021, v. 20, n. 2, p. 141, doi. 10.1142/S273741652042003X

By:

Cvitkovic, John P.;
Pauplis, Connor D.;
Carney, Phoebe C.;
Kaminski, George A.

Publication type:

Article

A Mathematical Model of Myosin Heavy Chain Dynamics in the Disintegration of Golden Threadfin Bream Nemipterus virgatus Surimi Gel.

Published in:

Gels (2310-2861), 2025, v. 11, n. 5, p. 348, doi. 10.3390/gels11050348

By:

Nakamizo, Ryoko;
Hayashi, Tatsuya;
Kominami, Yuri;
Ushio, Hideki

Publication type:

Article

Protein structure analysis of abnormal hemoglobins; Hb D-Los Angeles, Hb S and Hb G-Coushatta.

Published in:

Medicine Science, 2024, v. 13, n. 2, p. 289, doi. 10.5455/medscience.2024.01.06

By:

Ozturk, Onur

Publication type:

Article

AMPGen: an evolutionary information-reserved and diffusion-driven generative model for de novo design of antimicrobial peptides.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08282-7

By:

Jin, Shuwen;
Zeng, Zihan;
Xiong, Xiyan;
Huang, Baicheng;
Tang, Li;
Wang, Hongsheng;
Ma, Xiao;
Tang, Xiaochun;
Shao, Guoqing;
Huang, Xingxu;
Lin, Feng

Publication type:

Article

TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07534-w

By:

Tahmid, Md Toki;
Hasan, A.K.M. Mehedi;
Bayzid, Md Shamsuzzoha

Publication type:

Article

超线性阻尼项和 Kirchhoff项对解衰减速率的影响.

Published in:

Journal of Jilin University (Science Edition) / Jilin Daxue Xuebao (Lixue Ban), 2025, v. 63, n. 1, p. 9, doi. 10.13413/j.cnki.jdxblxb.2024467

By:

李仲庆;
郭斌;
高文杰

Publication type:

Article

两类蛋白质粗粒化模型.

Published in:

Journal of Jilin University (Science Edition) / Jilin Daxue Xuebao (Lixue Ban), 2025, v. 63, n. 1, p. 182, doi. 10.13413/j.cnki.jdxblxb.2024471

By:

史绍康;
赵莉;
吕中元

Publication type:

Article

人参皂苷Rg2通过PI3K/AKT/NF-kB信号通路减轻 LPS诱导的RAW264.7细胞炎症.

Published in:

Modern Food Science & Technology, 2024, v. 40, n. 12, p. 1, doi. 10.13982/j.mfst.1673-9078.2024.12.0016

By:

谢静;
袁巧云;
何姿良;
杨贵贵;
高翔;
张雯霞;
张迹;
胡卫成

Publication type:

Article

Modelizar y construir representaciones externas sobre la síntesis de proteínas: un estudio de diseño en la escuela secundaria.

Published in:

Didáctica de las Ciencias Experimentales y Sociales, 2022, n. 42, p. 119, doi. 10.7203/DCES.42.20945

By:

Occelli, Maricel;
Pomar, Susana;
Adrianna Gómez Galindo, Alma

Publication type:

Article

Association of a Novel Homozygous Variant in ABCA1 Gene with Tangier Disease.

Published in:

Journal of Clinical Medicine, 2023, v. 12, n. 7, p. 2596, doi. 10.3390/jcm12072596

By:

Barbosa-Gouveia, Sofía;
Fernández-Crespo, Silvia;
Lazaré-Iglesias, Héctor;
González-Quintela, Arturo;
Vázquez-Agra, Néstor;
Hermida-Ameijeiras, Álvaro

Publication type:

Article

Composition of Milk as Explained by Rumen Fermentation Parameters, Diet Composition and Combination.

Published in:

Journal of Animal Science, 2022, v. 100, p. 364, doi. 10.1093/jas/skac247.665

By:

Sujani, Sathya;
White, Robin R.

Publication type:

Article

43 Commercial realities of amino acid nutrition in the young pig.

Published in:

Journal of Animal Science, 2019, v. 97, p. 23, doi. 10.1093/jas/skz122.044

By:

Cook, David A;
Pilcher, Chad;
Humphrey, Brooke

Publication type:

Article

The impact of β-glucan on the stability of model dairy protein dispersions.

Published in:

Journal of Animal Science, 2006, v. 84, p. 175

By:

Bock, J. E.;
Schmidt, K. A.;
Milliken, G. E.

Publication type:

Article

Effects of replacement of animal protein with soy protein in lactating Holstein cows.

Published in:

Journal of Animal Science, 2006, v. 84, p. 80

By:

Garcia, A.;
Jardon, P. W.;
Patton, R. A.

Publication type:

Article

Möbius Transformation-Induced Distributions Provide Better Modelling for Protein Architecture.

Published in:

Mathematics (2227-7390), 2021, v. 9, n. 21, p. 2749, doi. 10.3390/math9212749

By:

Arashi, Mohammad;
Nakhaei Rad, Najmeh;
Bekker, Andriette;
Schubert, Wolf-Dieter

Publication type:

Article

Domain Heuristic Fusion of Multi-Word Embeddings for Nutrient Value Prediction.

Published in:

Mathematics (2227-7390), 2021, v. 9, n. 16, p. 1941, doi. 10.3390/math9161941

By:

Ispirova, Gordana;
Eftimov, Tome;
Koroušić Seljak, Barbara

Publication type:

Article

Challenges in the Computational Modeling of the Protein Structure—Activity Relationship.

Published in:

Computation, 2021, v. 9, n. 4, p. 39, doi. 10.3390/computation9040039

By:

Del Río, Gabriel

Publication type:

Article

Targeting Pro-Oxidant Iron with Exogenously Administered Apotransferrin Provides Benefits Associated with Changes in Crucial Cellular Iron Gate Protein TfR in a Model of Intracerebral Hemorrhagic Stroke in Mice.

Published in:

Antioxidants, 2023, v. 12, n. 11, p. 1945, doi. 10.3390/antiox12111945

By:

García-Serran, Alexia;
Ordoño, Jesús;
DeGregorio-Rocasolano, Núria;
Melià-Sorolla, Marc;
Odendaal, Karla;
Martí-Sistac, Octavi;
Gasull, Teresa

Publication type:

Article

How microwaves can help to study membrane ageing.

Published in:

Environmental Technology, 2020, v. 41, n. 18, p. 2314, doi. 10.1080/09593330.2018.1564072

By:

Rabiller-Baudry, M.;
Paquin, L.;
Lepéroux, C.;
Diallo, H.;
Al Jawad, H.;
Sepré, C.

Publication type:

Article

Laparoscopic lavage in a purulent peritonitis model: impact on inflammatory proteins.

Published in:

European Journal of Medical Research, 2025, v. 30, n. 1, p. 1, doi. 10.1186/s40001-025-02445-2

By:

Sinclair, Erik;
Magnusson, Maria K.;
Angenete, Eva;
Prytz, Mattias;
Tasselius, Viktor;
Öhman, Lena;
Haglind, Eva

Publication type:

Article

Accurate prediction of CDR-H3 loop structures of antibodies with deep learning.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.91512

By:

Hedi Chen;
Xiaoyu Fan;
Shuqian Zhu;
Yuchan Pei;
Xiaochun Zhang;
Xiaonan Zhang;
Lihang Liu;
Feng Qian;
Boxue Tian

Publication type:

Article

Sensitive remote homology search by local alignment of small positional embeddings from protein language models.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.91415

By:

Johnson, Sean R.;
Peshwa, Meghana;
Zhiyi Sun

Publication type:

Article

Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation, and virulence.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.84427

By:

Wei-Sheng Sun;
Lassinantti, Lena;
Järvå, Michael;
Schmitt, Andreas;
ter Beek, Josy;
Berntsson, Ronnie P.-A.

Publication type:

Article

Estimating the true stability of the prehydrolytic outward-facing state in an ABC protein.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.90736

By:

Simon, Márton A.;
Iordanov, Iordan;
Szollosi, Andras;
Csanády, László

Publication type:

Article

Liquid Plasticine‐Based Electrokinetic Enrichment of Proteins.

Published in:

ChemistryOpen, 2023, v. 12, n. 3, p. 1, doi. 10.1002/open.202200259

By:

Zhou, Yulin;
Niu, Jicheng;
Zhou, Yan;
Li, Fei

Publication type:

Article

Mesoporous Silica Nanoparticles Functionalized with Amino Groups for Biomedical Applications.

Published in:

ChemistryOpen, 2021, v. 10, n. 12, p. 1251, doi. 10.1002/open.202100227

By:

Estevão, Bianca Martins;
Miletto, Ivana;
Hioka, Noboru;
Marchese, Leonardo;
Gianotti, Enrica

Publication type:

Article

Directed Electron Transfer in Flavin Peptides with Oligoproline‐Type Helical Conformation as Models for Flavin‐Functional Proteins.

Published in:

ChemistryOpen, 2020, v. 9, n. 12, p. 1264, doi. 10.1002/open.202000199

By:

Wörner, Samantha;
Leier, Julia;
Michenfelder, Nadine C.;
Unterreiner, Andreas‐Neil;
Wagenknecht, Hans‐Achim

Publication type:

Article

PIPENN-EMB ensemble net and protein embeddings generalise protein interface prediction beyond homology.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-88445-y

By:

Thomas, David P. G.;
Garcia Fernandez, Carlos M.;
Haydarlou, Reza;
Feenstra, K. Anton

Publication type:

Article

Conjugation of Anti-EpCAM Antibody on Alginate-RIP MJ-30 Nanoparticle through Carbodiimide Reaction as a Model of Targeted Protein Therapy.

Published in:

Indonesian Journal of Pharmacy / Majalah Farmasi Indonesia, 2019, v. 30, n. 1, p. 52, doi. 10.14499/indonesianjpharm30iss1pp52

By:

Hilda Ismail;
Ummi H. Ciptasari;
M. Arief Nur Ikhsan;
Fidya Suryani;
Sismindari;
Ronny Martien;
Agustinus Yuswanto

Publication type:

Article

PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure.

Published in:

GigaScience, 2024, v. 13, n. 1, p. 1, doi. 10.1093/gigascience/giae104

By:

Ji, Yongxin;
Shang, Jiayu;
Guan, Jiaojiao;
Zou, Wei;
Liao, Herui;
Tang, Xubo;
Sun, Yanni

Publication type:

Article

Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants.

Published in:

GigaScience, 2024, v. 13, n. 1, p. 1, doi. 10.1093/gigascience/giae017

By:

Yang, Yiyan;
Dufault-Thompson, Keith;
Yan, Wei;
Cai, Tian;
Xie, Lei;
Jiang, Xiaofang

Publication type:

Article

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac118

By:

Varadi, Mihaly;
Nair, Sreenath;
Sillitoe, Ian;
Tauriello, Gerardo;
Anyango, Stephen;
Bienert, Stefan;
Borges, Clemente;
Deshpande, Mandar;
Green, Tim;
Hassabis, Demis;
Hatos, Andras;
Hegedus, Tamas;
Hekkelman, Maarten L;
Joosten, Robbie;
Jumper, John;
Laydon, Agata;
Molodenskiy, Dmitry;
Piovesan, Damiano;
Salladini, Edoardo;
Salzberg, Steven L

Publication type:

Article