Works matching Protein structure

Results: 5000

Artificial intelligence in fusion protein three‐dimensional structure prediction: Review and perspective.

Published in:

Clinical & Translational Medicine, 2024, v. 14, n. 8, p. 1, doi. 10.1002/ctm2.1789

By:

Kumar, Himansu;
Kim, Pora

Publication type:

Article

A Deep Learning Approach for Prediction of Protein Secondary Structure.

Published in:

Computers, Materials & Continua, 2022, v. 72, n. 2, p. 3705, doi. 10.32604/cmc.2022.026408

By:

Zubair, Muhammad;
Hanif, Muhammad Kashif;
Alabdulkreem, Eatedal;
Ghadi, Yazeed;
Khan, Muhammad Irfan;
Sarwar, Muhammad Umer;
Hanif, Ayesha

Publication type:

Article

Automated Protein Secondary Structure Assignment from C α Positions Using Neural Networks.

Published in:

Biomolecules (2218-273X), 2022, v. 12, n. 6, p. 841, doi. 10.3390/biom12060841

By:

Saqib, Mohammad N.;
Kryś, Justyna D.;
Gront, Dominik

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

Effective Local and Secondary Protein Structure Prediction by Combining a Neural Network-Based Approach with Extensive Feature Design and Selection without Reliance on Evolutionary Information.

Published in:

International Journal of Molecular Sciences, 2023, v. 24, n. 21, p. 15656, doi. 10.3390/ijms242115656

By:

Milchevskiy, Yury V.;
Milchevskaya, Vladislava Y.;
Nikitin, Alexei M.;
Kravatsky, Yury V.

Publication type:

Article

Building maps of protein structure spaces in template-free protein structure prediction.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019400134

By:

Zaman, Ahmed Bin;
Shehu, Amarda

Publication type:

Article

A self-adaptive evolutionary algorithm using Monte Carlo Fragment insertion and conformation clustering for the protein structure prediction problem.

Published in:

Natural Computing, 2024, v. 23, n. 4, p. 687, doi. 10.1007/s11047-022-09916-z

By:

Parpinelli, Rafael Stubs;
Will, Nilcimar Neitzel;
da Silva, Renan Samuel

Publication type:

Article

Artificial intelligence for template-free protein structure prediction: a comprehensive review.

Published in:

Artificial Intelligence Review, 2023, v. 56, n. 8, p. 7665, doi. 10.1007/s10462-022-10350-x

By:

Mufassirin, M. M. Mohamed;
Newton, M. A. Hakim;
Sattar, Abdul

Publication type:

Article

Energy Profile Bayes and Thompson Optimized Convolutional Neural Network protein structure prediction.

Published in:

Neural Computing & Applications, 2023, v. 35, n. 2, p. 1983, doi. 10.1007/s00521-022-07868-0

By:

Nallasamy, Varanavasi;
Seshiah, Malarvizhi

Publication type:

Article

Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE).

Published in:

PLoS ONE, 2019, v. 14, n. 2, p. 1, doi. 10.1371/journal.pone.0211043

By:

Téletchéa, S.;
Santuz, H.;
Léonard, S.;
Etchebest, C.

Publication type:

Article

DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure.

Published in:

PLoS ONE, 2019, v. 14, n. 01, p. 1, doi. 10.1371/journal.pone.0205214

By:

Ji, Shuangxi;
Oruç, Tuğçe;
Mead, Liam;
Rehman, Muhammad Fayyaz;
Thomas, Christopher Morton;
Butterworth, Sam;
Winn, Peter James

Publication type:

Article

De novo protein structure prediction using ultra-fast molecular dynamics simulation.

Published in:

PLoS ONE, 2018, v. 13, n. 11, p. 1, doi. 10.1371/journal.pone.0205819

By:

Cheung, Ngaam J.;
Yu, Wookyung

Publication type:

Article

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases.

Published in:

PLoS ONE, 2018, v. 13, n. 10, p. 1, doi. 10.1371/journal.pone.0206369

By:

Bittrich, Sebastian;
Schroeder, Michael;
Labudde, Dirk

Publication type:

Article

Multi-criteria protein structure comparison and structural similarities analysis using pyMCPSC.

Published in:

PLoS ONE, 2018, v. 13, n. 10, p. 1, doi. 10.1371/journal.pone.0204587

By:

Sharma, Anuj;
Manolakos, Elias S.

Publication type:

Article

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation.

Published in:

PLoS ONE, 2018, v. 13, n. 6, p. 1, doi. 10.1371/journal.pone.0197176

By:

Korkmaz, Selcuk;
Duarte, Jose M.;
Prlić, Andreas;
Goksuluk, Dincer;
Zararsiz, Gokmen;
Saracbasi, Osman;
Burley, Stephen K.;
Rose, Peter W.

Publication type:

Article

Porter 6: Protein Secondary Structure Prediction by Leveraging Pre-Trained Language Models (PLMs).

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 1, p. 130, doi. 10.3390/ijms26010130

By:

Alanazi, Wafa;
Meng, Di;
Pollastri, Gianluca

Publication type:

Article

AttSec: protein secondary structure prediction by capturing local patterns from attention map.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05310-3

By:

Kim, Youjin;
Kwon, Junseok

Publication type:

Article

Automated Procedure for Contact-Map-Based Protein Structure Reconstruction.

Published in:

Journal of Membrane Biology, 2014, v. 247, n. 5, p. 409, doi. 10.1007/s00232-014-9648-x

By:

Konopka, Bogumil;
Ciombor, Marika;
Kurczynska, Monika;
Kotulska, Malgorzata

Publication type:

Article

PROTEIN STRUCTURE PREDICTION: AN IN-DEPTH COMPARISON OF APPROACHES AND TOOLS.

Published in:

Eskişehir Technical University Journal of Science & Technology C - Life Sciences & Biotechnology, 2024, v. 13, n. 1, p. 30, doi. 10.18036/estubtdc.1378676

By:

ALTUNKÜLAH, Elif;
ENSARİ, Yunus

Publication type:

Article

АНАЛІЗ БІЛКОВИХ СТРУКТУР ПЛАЗМИ КРОВІ ПРИ ГЛІОМАХ З ВИКОРИСТАННЯМ БАЕСОВИХ ПРОЦЕДУР РОЗПІЗНАВАННЯ НА МОДЕЛЯХ ЛАНЦЮГІВ МАРКОВА.

Published in:

Cybernetics & Systems Analysis / Kibernetiki i Sistemnyj Analiz, 2022, v. 58, n. 4, p. 32

By:

ГУПАЛ, А. М.;
ТАРАСОВ, А. Л.

Publication type:

Article

БАЕСОВI ПРОЦЕДУРИ РОЗПIЗНАВАННЯ ДЛЯ АНАЛI3У БЁЛКОВИХ СТРУТКУР ПЛАЗМИ KPOBI ЗА ПОКАЗНИКАМИ ЛАЗЕРНОГО СПЕКТРОГРАФА У ПАЦIЕНТ1В 3 ПУХЛИНАМИ ГОЛОВНОГО МОЗКУ.

Published in:

Cybernetics & Systems Analysis / Kibernetiki i Sistemnyj Analiz, 2022, v. 58, n. 3, p. 42

By:

ГУПАЛ, А. М.;
ТАРАСОВ, А. Л.

Publication type:

Article

The epigenetic dimension of protein structure.

Published in:

Biomolecular Concepts, 2022, v. 13, n. 1, p. 55, doi. 10.1515/bmc-2022-0006

By:

Azzaz, Fodil;
Fantini, Jacques

Publication type:

Article

BDM: An Assessment Metric for Protein Complex Structure Models Based on Distance Difference Matrix.

Published in:

Interdisciplinary Sciences: Computational Life Sciences, 2024, v. 16, n. 3, p. 677, doi. 10.1007/s12539-024-00622-1

By:

Zhai, Jiaqi;
Wang, Wenda;
Zhao, Ranxi;
Sun, Daiwen;
Lu, Da;
Gong, Xinqi

Publication type:

Article

Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction.

Published in:

PLoS ONE, 2014, v. 9, n. 10, p. 1, doi. 10.1371/journal.pone.0109832

By:

Li, Qiwei;
Dahl, David B.;
Vannucci, Marina;
Hyun Joo;
Tsai, Jerry W.

Publication type:

Article

Atomic Resolution Structure of a Protein Prepared by Non-Enzymatic His-Tag Removal. Crystallographic and NMR Study of GmSPI-2 Inhibitor.

Published in:

PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0106936

By:

Kopera, Edyta;
Bal, Wojciech;
Lenarčič Živkovič, Martina;
Dvornyk, Angela;
Kludkiewicz, Barbara;
Grzelak, Krystyna;
Zhukov, Igor;
Zagórski-Ostoja, Włodzimierz;
Jaskolski, Mariusz;
Krzywda, Szymon

Publication type:

Article

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome.

Published in:

PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0096694

By:

Zhao, Huiying;
Wang, Jihua;
Zhou, Yaoqi;
Yang, Yuedong

Publication type:

Article

A new clustering and nomenclature for beta turns derived from high-resolution protein structures.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006844

By:

Shapovalov, Maxim;
Vucetic, Slobodan;
Jr.Dunbrack, Roland L.

Publication type:

Article

Automated evaluation of quaternary structures from protein crystals.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 5, p. 1, doi. 10.1371/journal.pcbi.1006104

By:

Bliven, Spencer;
Lafita, Aleix;
Parker, Althea;
Capitani, Guido;
Duarte, Jose M.

Publication type:

Article

Assigning secondary structure in proteins using AI.

Published in:

Journal of Molecular Modeling, 2021, v. 27, n. 9, p. 1, doi. 10.1007/s00894-021-04825-x

By:

Antony, Jisna Vellara;
Madhu, Prayagh;
Balakrishnan, Jayaraj Pottekkattuvalappil;
Yadav, Hemant

Publication type:

Article

Improved 3-D Protein Structure Predictions using Deep ResNet Model.

Published in:

Protein Journal, 2021, v. 40, n. 5, p. 669, doi. 10.1007/s10930-021-10016-7

By:

Geethu, S.;
Vimina, E. R.

Publication type:

Article

Bhageerath-Targeting the near impossible: Pushing the frontiers of atomic models for protein tertiary structure prediction.

Published in:

Journal of Chemical Sciences, 2012, v. 124, n. 1, p. 83, doi. 10.1007/s12039-011-0189-x

By:

JAYARAM, B;
DHINGRA, PRIYANKA;
LAKHANI, BHARAT;
SHEKHAR, SHASHANK

Publication type:

Article

Method to Generate Complex Predictive Features for Machine Learning-Based Prediction of the Local Structure and Functions of Proteins.

Published in:

Molecular Biology, 2023, v. 57, n. 1, p. 136, doi. 10.1134/S0026893323010089

By:

Milchevskiy, Yu. V.;
Milchevskaya, V. Yu.;
Kravatsky, Yu. V.

Publication type:

Article

Multistage Combination Classifier Augmented Model for Protein Secondary Structure Prediction.

Published in:

Frontiers in Genetics, 2022, p. 1, doi. 10.3389/fgene.2022.769828

By:

Zhang, Xu;
Liu, Yiwei;
Wang, Yaming;
Zhang, Liang;
Feng, Lin;
Jin, Bo;
Zhang, Hongzhe

Publication type:

Article

Global computational mutagenesis provides a critical stability framework in protein structures.

Published in:

PLoS ONE, 2017, v. 12, n. 12, p. 1, doi. 10.1371/journal.pone.0189064

By:

McCafferty, Caitlyn L.;
Sergeev, Yuri V.

Publication type:

Article

Protein asparagine deamidation prediction based on structures with machine learning methods.

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0181347

By:

Jia, Lei;
Sun, Yaxiong

Publication type:

Article

Impact of genetic variation on three dimensional structure and function of proteins.

Published in:

PLoS ONE, 2017, v. 12, n. 3, p. 1, doi. 10.1371/journal.pone.0171355

By:

Bhattacharya, Roshni;
Rose, Peter W.;
Burley, Stephen K.;
Prlić, Andreas

Publication type:

Article

Critical Features of Fragment Libraries for Protein Structure Prediction.

Published in:

PLoS ONE, 2017, v. 12, n. 1, p. 1, doi. 10.1371/journal.pone.0170131

By:

Trevizani, Raphael;
Custódio, Fábio Lima;
dos Santos, Karina Baptista;
Dardenne, Laurent Emmanuel

Publication type:

Article

SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity.

Published in:

Source Code for Biology & Medicine, 2018, v. 13, n. 1, p. N.PAG

By:

Liu, Tong;
Wang, Zheng

Publication type:

Article

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae006

By:

Zheng, Lingyan;
Shi, Shuiyang;
Sun, Xiuna;
Lu, Mingkun;
Liao, Yang;
Zhu, Sisi;
Zhang, Hongning;
Pan, Ziqi;
Fang, Pan;
Zeng, Zhenyu;
Li, Honglin;
Li, Zhaorong;
Xue, Weiwei;
Zhu, Feng

Publication type:

Article

GraphGPSM: a global scoring model for protein structure using graph neural networks.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad219

By:

He, Guangxing;
Liu, Jun;
Liu, Dong;
Zhang, Guijun

Publication type:

Article

Construct a variable-length fragment library for de novo protein structure prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac086

By:

Feng, Qiongqiong;
Hou, Minghua;
Liu, Jun;
Zhao, Kailong;
Zhang, Guijun

Publication type:

Article

Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac026

By:

Zhang, Biao;
Liu, Dong;
Zhang, Yang;
Shen, Hong-Bin;
Zhang, Gui-Jun

Publication type:

Article

tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab493

By:

Tran, Ngoc Hieu;
Xu, Jinbo;
Li, Ming

Publication type:

Article

Multi contact-based folding method for de novo protein structure prediction.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab463

By:

Hou, Minghua;
Peng, Chunxiang;
Zhou, Xiaogen;
Zhang, Biao;
Zhang, Guijun

Publication type:

Article

The Epigenetic Dimension of Protein Structure Is an Intrinsic Weakness of the AlphaFold Program.

Published in:

Biomolecules (2218-273X), 2022, v. 12, n. 10, p. N.PAG, doi. 10.3390/biom12101527

By:

Azzaz, Fodil;
Yahi, Nouara;
Chahinian, Henri;
Fantini, Jacques

Publication type:

Article

Deep Ensemble Learning with Atrous Spatial Pyramid Networks for Protein Secondary Structure Prediction.

Published in:

Biomolecules (2218-273X), 2022, v. 12, n. 6, p. 774, doi. 10.3390/biom12060774

By:

Guo, Yuzhi;
Wu, Jiaxiang;
Ma, Hehuan;
Wang, Sheng;
Huang, Junzhou

Publication type:

Article

AlphaFold-Predicted Structures of KCTD Proteins Unravel Previously Undetected Relationships among the Members of the Family.

Published in:

Biomolecules (2218-273X), 2021, v. 11, n. 12, p. 1862, doi. 10.3390/biom11121862

By:

Esposito, Luciana;
Balasco, Nicole;
Smaldone, Giovanni;
Berisio, Rita;
Ruggiero, Alessia;
Vitagliano, Luigi

Publication type:

Article

Discovering the Ultimate Limits of Protein Secondary Structure Prediction.

Published in:

Biomolecules (2218-273X), 2021, v. 11, n. 11, p. 1627, doi. 10.3390/biom11111627

By:

Ho, Chia-Tzu;
Huang, Yu-Wei;
Chen, Teng-Ruei;
Lo, Chia-Hua;
Lo, Wei-Cheng

Publication type:

Article

Protein secondary structure prediction by a neural network architecture with simple positioning algorithm techniques.

Published in:

International Journal of Electrical & Computer Engineering (2088-8708), 2022, v. 12, n. 4, p. 4380, doi. 10.11591/ijece.v12i4.pp4380-4390

By:

Ema, Romana Rahman;
Sultana, Sharmin;
Shaj, Shakil Ahmed;
Galib, Syed Md.

Publication type:

Article