Works matching DE "PROTEIN structure prediction"

Results: 585

Adaptive gradient scaling: integrating Adam and landscape modification for protein structure prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06185-2

By:

Kapitan, Vitalii;
Choi, Michael

Publication type:

Article

A General Substitution Matrix for Structural Phylogenetics Open Access.

Published in:

Molecular Biology & Evolution, 2025, v. 42, n. 6, p. 1, doi. 10.1093/molbev/msaf124

By:

Garg, Sriram G;
Hochberg, Georg K A

Publication type:

Article

Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes Open Access.

Published in:

Genome Biology & Evolution, 2025, v. 17, n. 6, p. 1, doi. 10.1093/gbe/evaf109

By:

Kim, Dongwook;
Park, Sukhwan;
Steinegger, Martin

Publication type:

Article

Multimodal AI in Biomedicine: Pioneering the Future of Biomaterials, Diagnostics, and Personalized Healthcare.

Published in:

Nanomaterials (2079-4991), 2025, v. 15, n. 12, p. 895, doi. 10.3390/nano15120895

By:

Parvin, Nargish;
Joo, Sang Woo;
Jung, Jae Hak;
Mandal, Tapas K.

Publication type:

Article

Molecular Insight into the Recognition of DNA by the DndCDE Complex in DNA Phosphorothioation.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 12, p. 5765, doi. 10.3390/ijms26125765

By:

Fu, Wencheng;
Wang, Yuli;
Ge, Yashi;
Gao, Haiyan;
Sun, Xuan;
Deng, Zixin;
Wang, Lianrong;
Chen, Shi;
He, Xinyi;
Wu, Geng

Publication type:

Article

Sequence-Based Prediction for Protein Solvent Accessibility.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 12, p. 5604, doi. 10.3390/ijms26125604

By:

Yang, Yang;
Chen, Mengqi;
Liu, Congrui;
Vihinen, Mauno

Publication type:

Article

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods.

Published in:

Cellulose, 2024, v. 31, n. 3, p. 1429, doi. 10.1007/s10570-023-05691-x

By:

Kwansa, Albert L.;
Singh, Abhishek;
Williams, Justin T.;
Haigler, Candace H.;
Roberts, Alison W.;
Yingling, Yaroslava G.

Publication type:

Article

Fragment-Based Protein Structure Prediction, Where Are We Now?

Published in:

Journal of Computational Biophysics & Chemistry, 2024, v. 23, n. 4, p. 441, doi. 10.1142/S2737416523300018

By:

Noor, Qudsia;
Kayode, Raheem;
Riaz, Rizwan;
Siddiqui, Areeba;
Mirza, Aiza Hassan;
Siddiqi, Abdul Rauf

Publication type:

Article

An End-to-End Deep Learning Pipeline for Assigning Secondary Structure in Proteins.

Published in:

Journal of Computational Biophysics & Chemistry, 2022, v. 21, n. 3, p. 335, doi. 10.1142/S2737416522500120

By:

Jisna, V. A.;
Jayaraj, P. B.

Publication type:

Article

Biologia strukturalna: historia, teraźniejszość i perspektywy.

Published in:

Nauka, 2023, n. 4, p. 17, doi. 10.24425/nauka.2023.148224

By:

JASKÓLSKI, MARIUSZ

Publication type:

Article

The Nobel Prize in Chemistry: past, present, and future of AI in biology.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07113-5

By:

Abriata, Luciano A.

Publication type:

Article

Data hazards in synthetic biology.

Published in:

Synthetic Biology (23977000), 2024, v. 9, n. 1, p. 1, doi. 10.1093/synbio/ysae010

By:

Zelenka, Natalie R;
Cara, Nina Di;
Sharma, Kieren;
Sarvaharman, Seeralan;
Ghataora, Jasdeep S;
Parmeggiani, Fabio;
Nivala, Jeff;
Abdallah, Zahraa S;
Marucci, Lucia;
Gorochowski, Thomas E

Publication type:

Article

The Organization and Function of the Phagophore-ER Membrane Contact Sites.

Published in:

Contact (25152564), 2023, v. 6, p. 1, doi. 10.1177/25152564231183898

By:

Duarte, Prado Vargas;
Reggiori, Fulvio

Publication type:

Article

Stranger Twins: A Tale of Resemblance and Contrast Between VAP Proteins.

Published in:

Contact (25152564), 2023, v. 6, p. 1, doi. 10.1177/25152564231183897

By:

Subra, Mélody;
Grimanelli, Zoé;
Gautier, Romain;
Mesmin, Bruno

Publication type:

Article

Mechanisms of Nonvesicular Ceramide Transport.

Published in:

Contact (25152564), 2023, v. 6, p. 1, doi. 10.1177/25152564231208250

By:

Clausmeyer, Lena;
Fröhlich, Florian

Publication type:

Article

Moving Lipids, by the Numbers.

Published in:

Contact (25152564), 2022, v. 5, p. 1, doi. 10.1177/25152564221103080

By:

Egea, Pascal F.

Publication type:

Article

猪内源性逆转录病毒在3种不同品系猪中的分布及序列特征研究.

Published in:

Chinese Journal of Preventive Veterinary Medicine / Zhongguo Yufang Shouyi Xuebao, 2022, v. 44, n. 11, p. 1141, doi. 10.3969/j.issn.1008-0589.202201027

By:

冯天悦;
Shah, Kamal;
张文立;
付利芝;
李昌文;
王玉娥;
陈洪岩

Publication type:

Article

RAMPing up knowledge of the translocon.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.98548

By:

VISMPAS, DIMITRIOS;
FÖRSTER, FRIEDRICH

Publication type:

Article

Protein language model-embedded geometric graphs power inter-protein contact prediction.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.92184

By:

Yunda Si;
Chengfei Yan

Publication type:

Article

How accurately can one predict drug binding modes using AlphaFold models?

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.89386

By:

Karelina, Masha;
Noh, Joseph J.;
Dror, Ron O.

Publication type:

Article

What AlphaFold tells us about cohesin's retention on and release from chromosomes.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.88656

By:

Nasmyth, Kim A.;
Lee, Byung-Gil;
Roig, Maurici Brunet;
Löwe, Jan

Publication type:

Article

In silico Discovery of RIOK3 Inhibitors Against Pancreatic Ductal Adenocarcinoma via Molecular Docking, Molecular Dynamics Simulations, and ADMET Prediction.

Published in:

Malaysian Journal of Medicine & Health Sciences, 2024, v. 20, p. 9

By:

Alhussinei, Kawthar;
Othman, Rozana;
Chuancheng Wei;
Abdullah, Iskandar;
Subramaniyan, Vetriselvan

Publication type:

Article

Severe deviation in protein fold prediction by advanced AI: a case study.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-89516-w

By:

López-Sagaseta, Jacinto;
Urdiciain, Alejandro

Publication type:

Article

ENABLEMENT AND WRITTEN DESCRIPTION BEYOND THE PROTEIN FOLDING HORIZON.

Published in:

Journal of Intellectual Property & Entertainment Law, 2024, v. 14, n. 1, p. 243

By:

LEE, ALEX

Publication type:

Article

Rapid Evolution in Action: Environmental Filtering Supports Coral Adaptation to a Hot, Acidic, and Deoxygenated Extreme Habitat.

Published in:

Global Change Biology, 2025, v. 31, n. 3, p. 1, doi. 10.1111/gcb.70103

By:

Leiva, Carlos;
Torda, Gergely;
Zhou, Chengran;
Pan, Yunrui;
Harris, Jess;
Xiang, Xueyan;
Tan, Shangjin;
Tian, Wei;
Hume, Benjamin;
Miller, David J.;
Li, Qiye;
Zhang, Guojie;
Cooke, Ira;
Rodolfo‐Metalpa, Riccardo

Publication type:

Article

Protein structure prediction via deep learning: an in-depth review.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1498662

By:

Meng, Yajie;
Zhang, Zhuang;
Zhou, Chang;
Tang, Xianfang;
Hu, Xinrong;
Tian, Geng;
Yang, Jialiang;
Yao, Yuhua

Publication type:

Article

Protein structure prediction via deep learning: an in-depth review.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1498662

By:

Meng, Yajie;
Zhang, Zhuang;
Zhou, Chang;
Tang, Xianfang;
Hu, Xinrong;
Tian, Geng;
Yang, Jialiang;
Yao, Yuhua

Publication type:

Article

Trends in the research and development of peptide drug conjugates: artificial intelligence aided design.

Published in:

2025

By:

Zhang, Dong-E;
He, Tong;
Shi, Tianyi;
Huang, Kun;
Peng, Anlin

Publication type:

Literature Review

Large language models facilitating modern molecular biology and novel drug development.

Published in:

2025

By:

Liu, Xiao-huan;
Lu, Zhen-hua;
Wang, Tao;
Liu, Fei

Publication type:

Literature Review

Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.

Published in:

Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1352703

By:

Greenshields-Watson, Alexander;
Abanades, Brennan;
Deane, Charlotte M.

Publication type:

Article

Sperm activate TLR2/TLR1 heterodimerization to induce a weak proinflammatory response in the bovine uterus.

Published in:

Frontiers in Immunology, 2023, p. 1, doi. 10.3389/fimmu.2023.1158090

By:

Mansouri, Alireza;
Yousef, Mohamed Samy;
Kowsar, Rasoul;
Usui, Nonoka;
Akthar, Ihshan;
Miyamoto, Akio

Publication type:

Article

Deep learning tools for advancing drug discovery and development.

Published in:

3 Biotech, 2022, v. 12, n. 5, p. 1, doi. 10.1007/s13205-022-03165-8

By:

Nag, Sagorika;
Baidya, Anurag T. K.;
Mandal, Abhimanyu;
Mathew, Alen T.;
Das, Bhanuranjan;
Devi, Bharti;
Kumar, Rajnish

Publication type:

Article

Deep learning tools for advancing drug discovery and development.

Published in:

3 Biotech, 2022, v. 12, n. 5, p. 1, doi. 10.1007/s13205-022-03165-8

By:

Nag, Sagorika;
Baidya, Anurag T. K.;
Mandal, Abhimanyu;
Mathew, Alen T.;
Das, Bhanuranjan;
Devi, Bharti;
Kumar, Rajnish

Publication type:

Article

A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-54668-2

By:

Soh, Timothy K.;
Ognibene, Sofia;
Sanders, Saskia;
Schäper, Robin;
Kaufer, Benedikt B.;
Bosse, Jens B.

Publication type:

Article

Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53761-w

By:

Jensvold, Zena D.;
Flood, Julia R.;
Christenson, Anna E.;
Lewis, Peter W.

Publication type:

Article

Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52951-w

By:

Mirabello, Claudio;
Wallner, Björn;
Nystedt, Björn;
Azinas, Stavros;
Carroni, Marta

Publication type:

Article

Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52951-w

By:

Mirabello, Claudio;
Wallner, Björn;
Nystedt, Björn;
Azinas, Stavros;
Carroni, Marta

Publication type:

Article

Histones and histone variant families in prokaryotes.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52337-y

By:

Schwab, Samuel;
Hu, Yimin;
van Erp, Bert;
Cajili, Marc K. M.;
Hartmann, Marcus D.;
Hernandez Alvarez, Birte;
Alva, Vikram;
Boyle, Aimee L.;
Dame, Remus T.

Publication type:

Article

Structure prediction of alternative protein conformations.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51507-2

By:

Bryant, Patrick;
Noé, Frank

Publication type:

Article

African Swine Fever Virus Protein–Protein Interaction Prediction.

Published in:

Viruses (1999-4915), 2024, v. 16, n. 7, p. 1170, doi. 10.3390/v16071170

By:

Fenster, Jacob A.;
Azzinaro, Paul A.;
Dinhobl, Mark;
Borca, Manuel V.;
Spinard, Edward;
Gladue, Douglas P.

Publication type:

Article

Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 12, p. 2440, doi. 10.3390/v15122440

By:

Mahony, Jennifer;
Goulet, Adeline;
van Sinderen, Douwe;
Cambillau, Christian

Publication type:

Article

Dynamic Evolution of SARS-CoV-2 in a Patient on Chemotherapy.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 8, p. 1759, doi. 10.3390/v15081759

By:

Huang, Weihua;
Yin, Changhong;
Briley, Kimberly P.;
Dalzell, William A. B.;
Fallon, John T.

Publication type:

Article

Advances in Structural Virology via Cryo-EM in 2022.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 6, p. 1315, doi. 10.3390/v15061315

By:

Schoehn, Guy;
Chenavier, Florian;
Crépin, Thibaut

Publication type:

Article

Structure Prediction and Analysis of Hepatitis E Virus Non-Structural Proteins from the Replication and Transcription Machinery by AlphaFold2.

Published in:

Viruses (1999-4915), 2022, v. 14, n. 7, p. N.PAG, doi. 10.3390/v14071537

By:

Goulet, Adeline;
Cambillau, Christian;
Roussel, Alain;
Imbert, Isabelle

Publication type:

Article

A Conserved Receptor-Binding Domain in the VP1u of Primate Erythroparvoviruses Determines the Marked Tropism for Erythroid Cells.

Published in:

Viruses (1999-4915), 2022, v. 14, n. 2, p. 420, doi. 10.3390/v14020420

By:

Bircher, Cornelia;
Bieri, Jan;
Assaraf, Ruben;
Leisi, Remo;
Ros, Carlos

Publication type:

Article

Protein secondary structure prediction (PSSP) using different machine algorithms.

Published in:

Egyptian Journal of Medical Human Genetics, 2021, v. 22, p. 1, doi. 10.1186/s43042-021-00173-w

By:

Afify, Heba M.;
Abdelhalim, Mohamed B.;
Mabrouk, Mai S.;
Sayed, Ahmed Y.

Publication type:

Article

Using AlphaFold to predict the impact of single mutations on protein stability and function.

Published in:

PLoS ONE, 2023, v. 18, n. 3, p. 1, doi. 10.1371/journal.pone.0282689

By:

Pak, Marina A.;
Markhieva, Karina A.;
Novikova, Mariia S.;
Petrov, Dmitry S.;
Vorobyev, Ilya S.;
Maksimova, Ekaterina S.;
Kondrashov, Fyodor A.;
Ivankov, Dmitry N.

Publication type:

Article

Analysing protein complexes in plant science: insights and limitation with AlphaFold 3.

Published in:

Botanical Studies, 2025, v. 66, n. 1, p. 1, doi. 10.1186/s40529-025-00462-2

By:

Lin, Pei-Yu;
Huang, Shiang-Chin;
Chen, Kuan-Lin;
Huang, Yu-Chun;
Liao, Chia-Yu;
Lin, Guan-Jun;
Lee, HueyTyng;
Chen, Pao-Yang

Publication type:

Article

Modeling orientational features via geometric algebra for 3D protein coordinates prediction.

Published in:

Mathematical Methods in the Applied Sciences, 2024, v. 47, n. 14, p. 11385, doi. 10.1002/mma.9608

By:

Pepe, Alberto;
Lasenby, Joan

Publication type:

Article

A nonsense mutation (c.382C>T) of PARN in a patient with idiopathic pulmonary fibrosis.

Published in:

QJM: An International Journal of Medicine, 2024, v. 117, n. 8, p. 605, doi. 10.1093/qjmed/hcae069

By:

Wang, Chen-Yu;
Liu, Lv;
Peng, Hong;
Luo, Hong

Publication type:

Article