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

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

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

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

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

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

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

Students' understanding of primary and secondary protein structure: Drawing secondary protein structure reveals student understanding better than simple recognition of structures.

Published in:

Biochemistry & Molecular Biology Education, 2013, v. 41, n. 6, p. 369, doi. 10.1002/bmb.20719

By:

Harle, Marissa;
Towns, Marcy H.

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

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

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure.

Published in:

BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-3491-0

By:

Abbass, Jad;
Nebel, Jean-Christophe

Publication type:

Article

ProteinNet: a standardized data set for machine learning of protein structure.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2932-0

By:

AlQuraishi, Mohammed

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

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

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

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

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

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

A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive.

Published in:

PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0161254

By:

Zhou, Ren-Bin;
Lu, Hui-Meng;
Liu, Jie;
Shi, Jian-Yu;
Zhu, Jing;
Lu, Qin-Qin;
Yin, Da-Chuan

Publication type:

Article

Addressing the Role of Conformational Diversity in Protein Structure Prediction.

Published in:

PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0154923

By:

Palopoli, Nicolas;
Monzon, Alexander Miguel;
Parisi, Gustavo;
Fornasari, Maria Silvina

Publication type:

Article

CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.

Published in:

PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0152517

By:

Fischer, Axel W.;
Heinze, Sten;
Putnam, Daniel K.;
Li, Bian;
Pino, James C.;
Xia, Yan;
Lopez, Carlos F.;
Meiler, Jens

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

利用粒子群算法在菱形网格上预测蛋白质结构.

Published in:

Chinese Journal of Bioinformatics, 2017, v. 15, n. 2, p. 105, doi. 10.3969/j.issn.1672-5565.20160702001

By:

陶凤英;
郭雨珍

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

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

FALCON2: a web server for high-quality prediction of protein tertiary structures.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04353-8

By:

Kong, Lupeng;
Ju, Fusong;
Zhang, Haicang;
Sun, Shiwei;
Bu, Dongbo

Publication type:

Article

FALCON2: a web server for high-quality prediction of protein tertiary structures.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04353-8

By:

Kong, Lupeng;
Ju, Fusong;
Zhang, Haicang;
Sun, Shiwei;
Bu, Dongbo

Publication type:

Article

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

Published in:

PLoS Computational Biology, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004889

By:

Jacquin, Hugo;
Gilson, Amy;
Shakhnovich, Eugene;
Cocco, Simona;
Monasson, Rémi

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

Transformer Encoder with Protein Language Model for Protein Secondary Structure Prediction.

Published in:

Engineering, Technology & Applied Science Research, 2024, v. 14, n. 2, p. 13124, doi. 10.48084/etasr.6855

By:

Kazm, Ammar;
Ali, Aida;
Hashim, Haslina

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

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

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

A-Prot: protein structure modeling using MSA transformer.

Published in:

BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04628-8

By:

Hong, Yiyu;
Lee, Juyong;
Ko, Junsu

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

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

3D Convolutional Neural Networks for Predicting Protein Structure for Improved Drug Recommendation.

Published in:

EAI Endorsed Transactions on Pervasive Health & Technology, 2024, v. 10, n. 1, p. 1, doi. 10.4108/eetpht.10.5685

By:

Sree, Pokkuluri Kiran;
N., S. S. S. N. Usha Devi

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

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

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