Protein structure prediction: when is it useful?

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

I-TASSER server for protein 3D structure prediction

Zhang, Y. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-40 · Cited by 5,124

TM-align: a protein structure alignment algorithm based on the TM-score

Zhang, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki524 · Cited by 3,774

The Universal Protein Resource (UniProt)

Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774

Scoring function for automated assessment of protein structure template quality

Zhang, Y., & Skolnick, J. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20264 · Cited by 2,392

The Universal Protein Resource (UniProt) in 2010

The UniProt Consortium (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp846 · Cited by 1,412

LGA: a method for finding 3D similarities in protein structures

Zemla, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg571 · Cited by 1,069

The Universal Protein Resource (UniProt)

The UniProt Consortium (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm895 · Cited by 824

LOMETS: A local meta-threading-server for protein structure prediction

Wu, S., & Zhang, Y. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm251 · Cited by 794

Composite Approaches to Protein Tertiary Structure Prediction: A Case‐Study by I‐Tasser

Roy, A., Wu, S., & Zhang, Y. (2010) · Wiley eBooks · doi:10.1002/9780470882207.ch11 · Cited by 3

Protein Tertiary Structures: Prediction from Amino Acid Sequences

Tress, M. L. (2013) · Wiley eBooks · doi:10.1002/9780470015902.a0003040.pub2 · Cited by 3

Hydrogen-Bonding Chains Twist the Peptide Bond as Revealed by Rotational Spectroscopy in N -Ethylformamide–Water Complexes

Jiang, N., Song, W., Hong, J., Zhou, M., & Li, W. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.5c17420 · Cited by 2

P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants

DeVoe, E., Oliver, G. R., Zenka, R. M., Blackburn, P. R., Cousin, M. A., Boczek, N. J., Kocher, J., Urrutia, R. A., Klee, E. W., & Zimmermann, M. T. (2021) · JAMIA Open · doi:10.1093/jamiaopen/ooab065 · Cited by 2

How the "folding funnel" depends on size and structure of proteins? a view from the scoring function perspective

Huang, S., & Springer, G. K. (2013) · Tsinghua Science & Technology · doi:10.1109/tst.2013.6616520 · Cited by 2

Cross-Species Insights into PR Proteins: A Comprehensive Study of Arabidopsis thaliana, Solanum lycopersicum, and Solanum tuberosum

Wilson, K., & Arunachalam, S. (2024) · Indian Journal of Microbiology · doi:10.1007/s12088-024-01343-1 · Cited by 2

Structure-based molecular docking approach for identifying S‑formylglutathione hydrolase from Sphingobium chungbukense

Lee, J.-P., Shin, W., Ahn, G., Um, H., Kim, Y., Kim, S. Y., Ahn, J., & Kim, Y. (2021) · Toxicology and Environmental Health Sciences · doi:10.1007/s13530-021-00109-2 · Cited by 2

Why Inverse Proteins Are Relatively Abundant

Nebel, J., & Walawage, C. G. C. (2010) · Protein and Peptide Letters · doi:10.2174/092986610791306698 · Cited by 2

Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules

Kelly, C. M., Muzard, J., Brooks, B. R., Lee, G. U., & Buchete, N. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp05307a · Cited by 2

Computational model for protein unfolding simulation

Tian, X.-H., Zheng, Y.-H., Jiao, X., Liu, C., & Chang, S. (2011) · Physical Review E · doi:10.1103/physreve.83.061910 · Cited by 2

Protein NMR Structures Refined without NOE Data

Ryu, H., Kim, T., Ahn, S., Ji, S., & Lee, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108888 · Cited by 2

Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states

Shirota, M., Ishida, T., & Kinoshita, K. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22982 · Cited by 2

Protein model quality assessment by learning-to-rank

Jing, X., Dong, Q., Liu, X., & Liu, B. (2015) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2015.7359660 · Cited by 2

In Silico Design of a Multimeric Polytope as a Highly Immunogenic DNA Vaccine Against Human Cytomegalovirus

Sabbaghian, E., Roodbari, F., Rafiei, A., & Amani, J. (2015) · Journal of Applied Biotechnology Reports · Cited by 2

Computational Modeling of Peptide-Protein Binding

Emery, J. S. (2010) · Cited by 2

Template-Based Protein Structure Prediction

Huang, J., Duan, P. W., & Wu, W. (2011) · Acta Biophysica Sinica · doi:10.3724/sp.j.1260.2011.00028 · Cited by 2

MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models

Virtanen, J. J., & Zhang, Y. (2018) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798318005612 · Cited by 2

An integrative bioinformatics analysis of caprine GNAI3 gene

Mishra, C., & Mohapatra, S. (2020) · Journal of Genetics · doi:10.1007/s12041-020-1183-1 · Cited by 2

Molecular characterization, putative structure and function, and expression profile of OAS1 gene in the endometrium of goats (Capra hircus)

Jain, A., Jain, T., Mishra, G. K., Chandrakar, K., Mukherjee, K., & Tiwari, S. P. (2023) · Reproductive Biology · doi:10.1016/j.repbio.2023.100760 · Cited by 2

Protein Tertiary Model Assessment Using Granular Machine Learning Techniques

Chida, A. A. (2022) · Digital Archive @ GSU · doi:10.57709/2723356 · Cited by 2

In silico prediction of prolactin molecules as a tool for equine genomics reproduction

Neis, A., Kremer, F. S., Pinto, L. D. S., & de Leon, P. M. M. (2019) · Molecular Diversity · doi:10.1007/s11030-018-09914-3 · Cited by 2

Integrative immunoinformatics and molecular modeling approaches for the rational design and in silico validation of a multi-epitope vaccine candidate against human herpesvirus 7

Latif, K., Ali, S. S., Khan, I., Almoghrabi-Ramirez, S., Khan, A. A., Iqbal, A., Agouni, A., & Haq, I. U. (2026) · Naunyn-Schmiedeberg s Archives of Pharmacology · doi:10.1007/s00210-026-05258-0 · Cited by 1

RNA viral protein structure database: A comprehensive and user‐friendly web database for RNA viral protein structures

Yang, Q., Tian, Z., Hu, T., Lou, J., Liu, H., Holmes, E. C., Shi, Y., Li, J., & Shi, W. (2026) · iMetaOmics. · doi:10.1002/imo2.70120 · Cited by 1

A novel protocol of energy optimisation for predicted protein structures built by homology modelling

Xu, T., Zhang, L., Wang, X., & Wei, D. (2010) · Molecular Simulation · doi:10.1080/08927022.2010.513771 · Cited by 1

MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map

Xu, D. H., & Zhang, Y. (2010) · Cited by 1

In vitro evaluation of a polytope DNA construct as a novel DNA vaccine strategy against human cytomegalovirus-associated diseases

Sabbaghian, E., Roodbari, F., Amani, J., & Rafiei, A. (2017) · Acta Virologica · doi:10.4149/av_2017_01_97 · Cited by 1

“The molecule’s the thing:” the promise of molecular modeling and dynamic simulations in aiding the prioritization and interpretation of genomic testing results

Oliver, G. R., Zimmermann, M. T., Klee, E. W., & Urrutia, R. A. (2016) · F1000Research · doi:10.12688/f1000research.8600.2 · Cited by 1

Overview of Protein Conjugation

(2011) · CRC Press eBooks · doi:10.1201/b11175-2 · Cited by 1

In-silico ab initio 3D structure prediction of goat kisspeptin precursor protein (135 amino acid residues)

Mukherjee, I., & Roy, I. (2022) · Indian Journal of Animal Health · doi:10.36062/ijah.2022.14022 · Cited by 1

Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy

Adiyaman, R., & McGuffin, L. J. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2974-1_7 · Cited by 1

Novel Protein Structure Prediction Model Using Fused Pipit Adapted Deep Convolutional Neural Network Classifier

Jadhav, S. S., & Vyavahare, A. J. (2023) · International Conference on Emerging Smart Computing and Informatics (ESCI) · doi:10.1109/esci56872.2023.10099768 · Cited by 1

A scoring function based on solvation thermodynamics for protein structure prediction

Du, S., Harano, Y., Kinoshita, M., & Sakurai, M. (2012) · BIOPHYSICS · doi:10.2142/biophysics.8.127 · Cited by 1

Structure‐based barcoding of proteins

Metri, R., Jerath, G., Kailas, G., Gacche, N., Pal, A., & Ramakrishnan, V. (2013) · Protein Science · doi:10.1002/pro.2392 · Cited by 1

Supercomputers in Modeling of Biological Systems

Maples, R., Ramasahayam, S., & Dumancas, G. G. (2015) · Advances in systems analysis, software engineering, and high performance computing book series · doi:10.4018/978-1-4666-7461-5.ch008 · Cited by 1

What is life?—70 years after Schrödinger

Niemi, A. J. (2017) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198785781.003.0013 · Cited by 1

Feature Importance in the Quality of Protein Templates

Adilović, M., & Hromić‐Jahjefendić, A. (2021) · Periodicals of Engineering and Natural Sciences (PEN) · doi:10.21533/pen.v9.i2.786 · Cited by 1

Structure, function and subcellular localization of the potato Resistance protein Rx1

Slootweg, E. J. (2009) · doi:10.18174/12671 · Cited by 1

Implementação de um framework de computação evolutiva multi-objetivo para predição Ab Initio da estrutura terciária de proteínas

Faccioli, R. A. (2012) · doi:10.11606/t.18.2012.tde-09052013-145839 · Cited by 1

Investigation of coiled-coil interactions between proteins of the spindle pole body

Zizlsperger, N. (2010) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 1

Molecular and Functional Characterisation of an Osmotin Gene from the Resurrection Plant Tripogon Loliiformis

Le, T. T. T. (2018) · Queensland University of Technology · doi:10.5204/thesis.eprints.115835 · Cited by 1

Single-molecule studies of prion protein folding and misfolding

Yu, H. (2013) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3k06x87j · Cited by 1

Molecules, cells and minds : aspects of bioscientific explanation

Powell, A. M. (2009) · UPT. Syiah Kuala University Library (Syiah Kuala University) · Cited by 1

Using pilot-jobs for developing eThread, a meta-threading pipeline

Ragothaman, A. (2014) · doi:10.7282/t337794m

CORE: Common Region Extension Based Multiple Protein Structure Alignment for Producing Multiple Solution

Kim, W.-C., Park, S., & Won, J.-I. (2013) · Journal of Computer Science and Technology · doi:10.1007/s11390-013-1365-x

Artificial neural networks for predicting 3D protein shapes from amino acid sequences

Viktor, H. L., Paquet, E., & Zhao, J. (2013) · International Joint Conference on Neural Networks (IJCNN) · doi:10.1109/ijcnn.2013.6706956

Protein structure prediction and structure -based protein function annotation

Roy, A. (2011) · KU ScholarWorks (The University of Kansas)

Protein Structure Prediction Based on Neural Networks

Zhao, J. (2013) · uO Research (University of Ottawa) · doi:10.20381/ruor-6390

Development of novel computational techniques for the study of biomolecular systems using molecular dynamics simulation

Mirjalili, V. (2014) · Michigan State University Libraries · doi:10.25335/6rcc-5254

Enhanced prediction of several protein structural attributes with machine learning algorithms

Yang, J. (2012) · doi:10.32657/10356/48058

Protein Function Prediction Based on Sequence and Structure Information

Smaili, F. Z. (2016) · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · doi:10.25781/kaust-z5074

Overview of Protein Conjugation

Wong, S. S., & Jameson, D. M. (2011) · CRC Press eBooks · doi:10.1201/b11175-4

Molecular characterization of phytoene desaturase (crti) gene from paracoccus bogoriensis

Kariuki, H. W. (2014)

Protein Structure Prediction Using CABS – A Consensus Approach

Błaszczyk, M., Jamróz, M. H., Gront, D., & Koliński, A. (2012)

Modelagem Molecular da Interação entre a Proteína de Fusão do Vírus Sincicial Respiratório Humano e Inibidores da Ação Viral

de Souza, F. P. (2012)

Application of Molecular Modelling to Speed-up the Lead Discovery Process

Trist, I. M. L., Botta, M., & Fallacara, A. L. (2017) · Royal Society of Chemistry eBooks · doi:10.1039/9781788010139-00281

Identification of Genetic and Protein Markers in Salmonella enterica serovar Typhimurium by Bioinformatic Analyses for the Purpose of Diagnosis and Treatment

Amandadi, M., Ravan, H., & Hassanshahian, M. (2017) · DOAJ (DOAJ: Directory of Open Access Journals)

Structural bioinformatics studies and tool development related to drug discovery

Hatherley, R. (2016)

Estimating Residue-Specific Accuracies of Protein Structure Models Using Molecular Dynamics SimulationsPreprint

Hu, J.-H., Xun, S., Wu, H., Wu, Y., & Jiang, F. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/439760

Desenvolvimento de nanodispositivos baseados em biomoléculas: abordagens computacionais

Franca, E. D. F., Oliveira, G. S., Ierich, J. C. M., Vig, A. C. A., Brandini, C. P., Moraes, A. D. S., & Leite, F. L. (2018) · doi:10.7476/9786580216123.0005

Insights into RNA structure by melding experiment and computation

Hajdin, C. E. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/tx6z-gh43

Computational Methods for Evaluation of Protein Structural Models

Alapati, R. (2019)

Molecular Modeling of the Interaction Between Stem Cell Peptide and Immune Receptor in Plants

Naseem, M., Srivastava, M., Osmanoğlu, Ö., Iqbal, J., Howari, F. M., AlRemeithi, F. A., & Dandekar, T. (2019) · Methods in molecular biology · doi:10.1007/978-1-0716-0183-9_8

Using physical features of protein core packing to distinguish real proteins from decoys

Grigas, A. T., Mei, Z., Treado, J. D., Levine, Z. A., Regan, L., & O’Hern, C. S. (2020) · Protein Science · doi:10.1002/pro.3914

The structure of the native α-synuclein ensemble determined using a combination of structural proteomics and discrete molecular dynamics simulations

Brodie, N. I. (2020) · Journal of Proteomics

Vitamin K and Vitamin K-Dependent Proteins in Relation to Human Health

Shearer, M. J., & Schurgers, L. J. (2018) · MDPI eBooks · doi:10.3390/books978-3-03842-832-9

Caracterização estrutural de Dectin-1 humana e análise de interação com seus alvos moleculares β-glucanos e Syk

Tamarozzi, E. R. (2020) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.17.2020.tde-09042021-094503

In silico analysis of bovine Glutathione-S-transferase M1 (GSTM1), an essential gene governing bull semen quality

Mukherjee, A., Kar, I., Das, S., Acharya, A. P., Maity, H. K., Biswas, P., & Biswas, S. (2021) · Indian Journal of Animal Health · doi:10.36062/ijah.2021.08321

Correlation of model quality between predicted proteins and their templates

Adilović, M., & Hromić‐Jahjefendić, A. (2022) · Periodicals of Engineering and Natural Sciences (PEN) · doi:10.21533/pen.v10.i1.553

Faculty Opinions recommendation of Highly accurate protein structure prediction for the human proteome.

Zhang, W., & Zhai, R. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.740510745.793587739

Faculty Opinions recommendation of Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

Dill, K. A., & Pérez, A. (2017) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727797185.793538420

Biotechnology in Medicine: Advances-II

Rajan, S., Bhat, A. H., Maity, S., & Thakur, O. (2022) · Springer eBooks · doi:10.1007/978-3-030-98554-7_4

Protein Structure Prediction: A Computational Approach to Unraveling Molecular Mysteries

Selwate, T., Kamble, M. A., Sabale, P., Dhabarde, D. M., Kalyani, D., & Baheti, J. (2025) · Algorithms for intelligent systems · doi:10.1007/978-981-96-1285-7_4

Computational geometry for the determination of biomolecular structures

Machat, M. (2017) · theses.fr (ABES) · doi:10.70675/db61d77dz78eez4af7zb195z36dda8fed2ed

Calcul efficace de la structure des protéines à partir de contacts évolutifs

Allain, F. (2017) · theses.fr (ABES) · doi:10.70675/0dc56133z00acz4dffz8c7az0533f04cf409

Caractérisation structurale et fonctionnelle de SpNox, une NADPH oxydase bactérienne

Vermot, A. (2020) · theses.fr (ABES) · doi:10.70675/8982dcf6zda88z4163z9743z5b4415e9889f

Protein Structure Prediction

Roy, A., & Zhang, Y. (2012) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0003031.pub2 · Cited by 12

Protein Three-Dimensional Structure Prediction

Abeln, S., Feenstra, K. A., & Heringa, J. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20505-0 · Cited by 9

Template-Based Protein Structure Prediction

Wu, W. (2011) · Acta Biophysica Sinica

Accurate protein structure prediction: what comes next?

Seok, C., Baek, M., Steinegger, M., Park, H., Lee, G. R., & Won, J. (2021) · Korean Society for Structural Biology · doi:10.34184/kssb.2021.9.3.47 · Cited by 75

Introduction to Protein Structure PredictionPreprint

Abeln, S., Heringa, J., & Feenstra, K. A. (2017) · arXiv (Cornell University) · doi:10.48550/arxiv.1712.00407