Works matching Protein structure

Results: 5000

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

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

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

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

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

Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction.

Published in:

Molecules, 2019, v. 24, n. 5, p. 854, doi. 10.3390/molecules24050854

By:

Kabir, Kazi Lutful;
Hassan, Liban;
Rajabi, Zahra;
Akhter, Nasrin;
Shehu, Amarda

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

Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures.

Published in:

Genome Biology & Evolution, 2025, v. 17, n. 2, p. 1, doi. 10.1093/gbe/evaf013

By:

Wright, Erik S

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

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

Recent Progress of Protein Tertiary Structure Prediction.

Published in:

Molecules, 2024, v. 29, n. 4, p. 832, doi. 10.3390/molecules29040832

By:

Wuyun, Qiqige;
Chen, Yihan;
Shen, Yifeng;
Cao, Yang;
Hu, Gang;
Cui, Wei;
Gao, Jianzhao;
Zheng, Wei

Publication type:

Article

Assessment of AI-Based Protein Structure Prediction for the NLRP3 Target.

Published in:

Molecules, 2022, v. 27, n. 18, p. 5797, doi. 10.3390/molecules27185797

By:

Yin, Jian;
Lei, Junkun;
Yu, Jialin;
Cui, Weiren;
Satz, Alexander L.;
Zhou, Yifan;
Feng, Hua;
Deng, Jason;
Su, Wenji;
Kuai, Letian

Publication type:

Article

CRFalign: A Sequence-Structure Alignment of Proteins Based on a Combination of HMM-HMM Comparison and Conditional Random Fields.

Published in:

Molecules, 2022, v. 27, n. 12, p. 3711, doi. 10.3390/molecules27123711

By:

Lee, Sung Jong;
Joo, Keehyoung;
Sim, Sangjin;
Lee, Juyong;
Lee, In-Ho;
Lee, Jooyoung

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

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

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

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

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

Published in:

Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1748-7188-8-5

By:

Xuefeng Cui;
Shuai Cheng Li;
Dongbo Bu;
Alipanahi, Babak;
Ming Li

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

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

RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures.

Published in:

Journal of Bioinformatics & Computational Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1142/S0219720023500014

By:

Sofi, Mukhtar Ahmad;
Wani, M. Arif

Publication type:

Article

Principal component analysis in protein tertiary structure prediction.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 2, p. -1, doi. 10.1142/S0219720018500051

By:

Álvarez, Óscar;
Fernández-Martínez, Juan Luis;
Fernández-Brillet, Celia;
Cernea, Ana;
Fernández-Muñiz, Zulima;
Kloczkowski, Andrzej

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

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

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

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

Prediction of protein secondary structure by the improved TCN-BiLSTM-MHA model with knowledge distillation.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-67403-0

By:

Zhao, Lufei;
Li, Jingyi;
Zhan, Weiqiang;
Jiang, Xuchu;
Zhang, Biao

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

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

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

Prediction of Protein Secondary Structure Based on WS-BiLSTM Model.

Published in:

Symmetry (20738994), 2022, v. 14, n. 1, p. 89, doi. 10.3390/sym14010089

By:

Gao, Yang;
Zhao, Yawu;
Ma, Yuming;
Liu, Yihui

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