Protein structure prediction: when is it useful?

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

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The Protein Data Bank

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I-TASSER server for protein 3D structure prediction

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

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 · see citing works

The Universal Protein Resource (UniProt)

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Scoring function for automated assessment of protein structure template quality

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The Universal Protein Resource (UniProt) in 2010

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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 · see citing works

The Universal Protein Resource (UniProt)

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

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 774 · see citing works

CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is expressed on tumor-associated vasculature

Miao, Z., Luker, K. E., Summers, B. C., Berahovich, R., Bhojani, M. S., Rehemtulla, A., Kleer, C. G., Essner, J. J., Nasevicius, A., Luker, G. D., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610444104 · Cited by 528 · see citing works

Ab initio modeling of small proteins by iterative TASSER simulations

Wu, S., Skolnick, J., & Zhang, Y. (2007) · BMC Biology · doi:10.1186/1741-7007-5-17 · Cited by 512 · see citing works

Progress and challenges in protein structure prediction

Zhang, Y. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.02.004 · Cited by 507 · see citing works

Template-based modeling and free modeling by I-TASSER in CASP7

Zhang, Y. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21702 · Cited by 467 · see citing works

The Impact of Structural Genomics: Expectations and Outcomes

Chandonia, J., & Brenner, S. E. (2006) · Science · doi:10.1126/science.1121018 · Cited by 377 · see citing works

In silicopharmacology for drug discovery: applications to targets and beyond

Ekins, S., Mestres, J., & Testa, B. (2007) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707306 · Cited by 367 · see citing works

Completeness in structural genomics.

Vitkup, D., Melamud, E., Moult, J., & Sander, C. (2001) · Nature Structural Biology · doi:10.1038/88640 · Cited by 348 · see citing works

Automated structure prediction of weakly homologous proteins on a genomic scale

Zhang, Y., & Skolnick, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0305695101 · Cited by 344 · see citing works

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

Brylinski, M., & Skolnick, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707684105 · Cited by 333 · see citing works

Critical assessment of methods of protein structure prediction—Round VII

Moult, J., Fidelis, K. A., Kryshtafovych, A., Rost, B., Hubbard, T., & Tramontano, A. L. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21767 · Cited by 321 · see citing works

High-resolution structure prediction and the crystallographic phase problem

Qian, B., Raman, S., Das, R., Bradley, P. H., McCoy, A. J., Read, R. J., & Baker, D. A. (2007) · Nature · doi:10.1038/nature06249 · Cited by 317 · see citing works

The protein structure prediction problem could be solved using the current PDB library

Zhang, Y., & Skolnick, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407152101 · Cited by 297 · see citing works

Identification and Analysis of Deleterious Human SNPs

Yue, P., & Moult, J. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.12.025 · Cited by 265 · see citing works

Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome

Zhang, Y., DeVries, M. E., & Skolnick, J. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020013 · Cited by 236 · see citing works

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

Das, R., Qian, B., Raman, S., Vernon, R. M., Thompson, J., Bradley, P. H., Khare, S. D., Tyka, M. D., Bhat, D., Chivian, D. C., et al. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21636 · Cited by 209 · see citing works

On the origin and highly likely completeness of single-domain protein structures

Zhang, Y., Hubner, I. A., Arakaki, A. K., Shakhnovich, E., & Skolnick, J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509379103 · Cited by 197 · see citing works

Assessment of CASP7 predictions for template‐based modeling targets

Kopp, J., Bordoli, L., Battey, J., Kiefer, F., & Schwede, T. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21753 · Cited by 170 · see citing works

Assessment of CASP7 structure predictions for template free targets

Jauch, R., Yeo, H. C., Kolatkar, P. R., & Clarke, N. D. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21771 · Cited by 160 · see citing works

Physically realistic homology models built with rosetta can be more accurate than their templates

Misura, K. M. S., Chivian, D. C., Rohl, C. A., Kim, D. E., & Baker, D. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509355103 · Cited by 156 · see citing works

Molecular dynamics in the endgame of protein structure prediction

Lee, M. R., Tsai, J. W., Baker, D. A., & Kollman, P. A. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5032 · Cited by 143 · see citing works

An Integrated in Silico 3D Model-Driven Discovery of a Novel, Potent, and Selective Amidosulfonamide 5-HT1A Agonist (PRX-00023) for the Treatment of Anxiety and Depression

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Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding

Zhang, Y., Kihara, D., & Skolnick, J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10141 · Cited by 139 · see citing works

Quantifying the Similarities within Fold Space

Harrison, A., Pearl, F. M. G., Mott, R., Thornton, J. M., & Orengo, C. A. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00992-0 · Cited by 137 · see citing works

Can molecular dynamics simulations provide high‐resolution refinement of protein structure?

Chen, J., & Brooks, C. L. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21345 · Cited by 130 · see citing works

The Universal Protein Resource (UniProt)

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Assessment of CASP7 predictions in the high accuracy template-based modeling category

Read, R. J., & Chavali, G. B. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21662 · Cited by 111 · see citing works

Prediction of global and local model quality in CASP7 using Pcons and ProQ

Wallner, B., & Elofsson, A. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21774 · Cited by 109 · see citing works

A multi-template combination algorithm for protein comparative modeling

Cheng, J. J. (2008) · BMC Structural Biology · doi:10.1186/1472-6807-8-18 · Cited by 90 · see citing works

Assessment of predictions submitted for the CASP7 domain prediction category

Tress, M. L., Cheng, J. J., Baldi, P., Joo, K., Lee, J., Seo, J., Lee, J., Baker, D. A., Chivian, D. C., Kim, D. E., et al. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21675 · Cited by 88 · see citing works

Servers for protein structure prediction

Fischer, D. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.03.004 · Cited by 87 · see citing works

Benchmarking consensus model quality assessment for protein fold recognition

McGuffin, L. J. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-345 · Cited by 80 · see citing works

Refining homology models by combining replica‐exchange molecular dynamics and statistical potentials

Zhu, J., Fan, H., Périole, X., Honig, B. H., & Mark, A. E. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22005 · Cited by 79 · see citing works

Can a physics‐based, all‐atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking

Wróblewska, L., & Skolnick, J. (2007) · Journal of Computational Chemistry · doi:10.1002/jcc.20720 · Cited by 67 · see citing works

Structural genomics analysis of alternative splicing and application to isoform structure modeling

Wang, P., Yan, B., Guo, J., Hicks, C., & Xu, Y. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506770102 · Cited by 67 · see citing works

Protein model refinement using an optimized physics-based all-atom force field

Jagielska, A., Wróblewska, L., & Skolnick, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800054105 · Cited by 66 · see citing works

Evaluating the usefulness of protein structure models for molecular replacement

Giorgetti, A., Raimondo, D., Miele, A. E., & Tramontano, A. L. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1112 · Cited by 66 · see citing works

Coordinated Up-regulation by Hypoxia of Adrenomedullin and One of Its Putative Receptors (RDC-1) in Cells of the Rat Blood-Brain Barrier

Ladoux, A., & Frelin, C. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m006512200 · Cited by 65 · see citing works

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment

Arakaki, A. K., Zhang, Y., & Skolnick, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth044 · Cited by 57 · see citing works

Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints

Bryliński, M., & Skolnick, J. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.20917 · Cited by 55 · see citing works

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

Malmström, L., Riffle, M. E., Strauss, C. E. M., Chivian, D. C., Davis, T. N., Bonneau, R., & Baker, D. A. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050076 · Cited by 52 · see citing works

A Random Mutagenesis Approach to Isolate Dominant-Negative Yeastsec1Mutants Reveals a Functional Role for Domain 3a in Yeast and Mammalian Sec1/Munc18 Proteins

Boyd, A., Ciufo, L. F., Barclay, J. W., Graham, M. E., Haynes, L. P., Doherty, M. K., Riesen, M., Burgoyne, R. D., & Morgan, A. (2008) · Genetics · doi:10.1534/genetics.108.090423 · Cited by 41 · see citing works

Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models

Wróblewska, L., Jagielska, A., & Skolnick, J. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.121947 · Cited by 38 · see citing works

Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential

Zhou, H., & Skolnick, J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21813 · Cited by 35 · see citing works

MODELING AND ANALYZING THREE-DIMENSIONAL STRUCTURES OF HUMAN DISEASE PROTEINS

Ye, Y., Li, Z., & Godzik, A. (2005) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812701626_0040 · Cited by 34 · see citing works

Update on the Protein Structure Initiative

Norvell, J. C., & Berg, J. M. (2007) · Structure · doi:10.1016/j.str.2007.11.004 · Cited by 33 · see citing works

Comparative Modeling in Structural Genomics

Moult, J. (2008) · Structure · doi:10.1016/j.str.2007.12.001 · Cited by 28 · see citing works

Applying undertaker cost functions to model quality assessment

Archie, J. G., & Karplus, K. J. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22288 · Cited by 18 · see citing works

I-TASSER: a unified platform for automated protein structure and function prediction

Roy, A., Küçükural, A., & Zhang, Y. (2010) · Nature Protocols · doi:10.1038/nprot.2010.5 · Cited by 6,093 · see citing works

Evolutionary-scale prediction of atomic level protein structure with a language model

Lin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., et al. (2022) · doi:10.1101/2022.07.20.500902 · Cited by 5,523 · see citing works

Improved protein structure prediction using potentials from deep learning

Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T., Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., et al. (2020) · Nature · doi:10.1038/s41586-019-1923-7 · Cited by 3,378 · see citing works

Highly accurate protein structure prediction for the human proteome

Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · see citing works

I-TASSER server: new development for protein structure and function predictions

Yang, J., & Zhang, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv342 · Cited by 2,486 · see citing works

How significant is a protein structure similarity with TM-score = 0.5?

Xu, J., & Zhang, Y. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq066 · Cited by 1,142 · see citing works

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

Xu, D. H., & Zhang, Y. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.10.024 · Cited by 1,027 · see citing works

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

Yang, J., Roy, A., & Zhang, Y. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt447 · Cited by 1,023 · see citing works

Molecular dynamics simulations: advances and applications

Gelpí, J. L., Hospital, A., Goñi, R., & Orozco, M. (2015) · Advances and Applications in Bioinformatics and Chemistry · doi:10.2147/aabc.s70333 · Cited by 951 · see citing works

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

Roy, A., Yang, J., & Zhang, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks372 · Cited by 695 · see citing works

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

Zhang, C., Freddolino, L., & Zhang, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx366 · Cited by 606 · see citing works

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

Zheng, W. H., Zhang, C., Li, Y., Pearce, R., Bell, E. W., & Zhang, Y. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100014 · Cited by 574 · see citing works

From Protein Engineering to Immobilization: Promising Strategies for the Upgrade of Industrial Enzymes

Singh, R. K., Tiwari, M. K., Singh, R., & Lee, J.-K. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms14011232 · Cited by 452 · see citing works

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

Raveh, B., London, N., & Schueler‐Furman, O. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22716 · Cited by 423 · see citing works

I‐TASSER: Fully automated protein structure prediction in CASP8

Zhang, Y. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22588 · Cited by 420 · see citing works

DRAMP 2.0, an updated data repository of antimicrobial peptides

Kang, X., Dong, F., Shi, C., Liu, S., Sun, J., Chen, J., Li, H., Xu, H., Lao, X., & Zheng, H. (2019) · Scientific Data · doi:10.1038/s41597-019-0154-y · Cited by 395 · see citing works

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

Zhang, J., Yu, L., & Zhang, Y. (2011) · Structure · doi:10.1016/j.str.2011.09.022 · Cited by 332 · see citing works

Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations

Raval, A., Piana, S., Eastwood, M. P., Dror, R. O., & Shaw, D. E. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24098 · Cited by 255 · see citing works

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

Zhang, J., & Zhang, Y. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015386 · Cited by 237 · see citing works

Three-dimensional protein structure prediction: Methods and computational strategies

Dorn, M., Silva, M. B. E., Buriol, L. S., & Lamb, L. C. (2014) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2014.10.001 · Cited by 210 · see citing works

Genomics and Bioinformatics Resources for Crop Improvement

Mochida, K., & Shinozaki, K. (2010) · Plant and Cell Physiology · doi:10.1093/pcp/pcq027 · Cited by 202 · see citing works

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

Mukherjee, S., & Zhang, Y. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp318 · Cited by 178 · see citing works

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

Sircar, A., & Gray, J. J. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000644 · Cited by 166 · see citing works

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities

Gallicchio, E., Lapelosa, M., & Levy, R. M. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct1002913 · Cited by 158 · see citing works

Automated protein structure modeling in CASP9 by I‐TASSER pipeline combined with QUARK‐based ab initio folding and FG‐MD‐based structure refinement

Xu, D. H., Zhang, J., Roy, A., & Zhang, Y. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23111 · Cited by 149 · see citing works

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto‐encoder deep neural network

Lyons, J., Dehzangi, A., Heffernan, R., Sharma, A. K., Paliwal, K. K., Sattar, A., Zhou, Y., & Yang, Y. (2014) · Journal of Computational Chemistry · doi:10.1002/jcc.23718 · Cited by 145 · see citing works

Old friends in new guise: repositioning of known drugs with structural bioinformatics

Haupt, V. J., & Schroeder, M. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr011 · Cited by 142 · see citing works

Effective protein model structure refinement by loop modeling and overall relaxation

Lee, G. R., Heo, L., & Seok, C. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24858 · Cited by 136 · see citing works

ResQ: An Approach to Unified Estimation of B -Factor and Residue-Specific Error in Protein Structure Prediction

Yang, J., Wang, Y., & Zhang, Y. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.09.024 · Cited by 132 · see citing works

REMO: A new protocol to refine full atomic protein models from C‐alpha traces by optimizing hydrogen‐bonding networks

Li, Y., & Zhang, Y. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22380 · Cited by 131 · see citing works

Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins

Geng, H. R., Chen, F., Ye, J., & Jiang, F. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.07.010 · Cited by 127 · see citing works

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

Nishi, H., Tyagi, M. G., Teng, S., Shoemaker, B. A., Hashimoto, K., Alexov, E. G., Wuchty, S., & Panchenko, A. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066273 · Cited by 117 · see citing works

Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER

Zheng, W. H., Wuyun, Q., Li, Y., Liu, Q., Zhou, X., Peng, C., Zhu, Y., Freddolino, L., & Zhang, Y. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02654-4 · Cited by 115 · see citing works

COMPUTATIONAL ENZYME DESIGN APPROACHES WITH SIGNIFICANT BIOLOGICAL OUTCOMES: PROGRESS AND CHALLENGES

Li, X., Zhang, Z., & Song, J. (2012) · Computational and Structural Biotechnology Journal · doi:10.5936/csbj.201209007 · Cited by 111 · see citing works

Conformation Dependence of Backbone Geometry in Proteins

Berkholz, D. S., Shapovalov, M. V., Dunbrack, R. L., & Karplus, P. A. (2009) · Structure · doi:10.1016/j.str.2009.08.012 · Cited by 107 · see citing works

On the significance of an RNA tertiary structure prediction

Hajdin, C. E., Ding, F., Dokholyan, N. V., & Weeks, K. M. (2010) · RNA · doi:10.1261/rna.1837410 · Cited by 106 · see citing works

Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

Mirjalili, V., Noyes, K., & Feig, M. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24336 · Cited by 101 · see citing works

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

Brodie, N. I., Popov, K. I., Petrotchenko, E. V., Dokholyan, N. V., & Borchers, C. H. (2017) · Science Advances · doi:10.1126/sciadv.1700479 · Cited by 100 · see citing works

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Zhang, C., Mortuza, S. M., He, B., Wang, Y., & Zhang, Y. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25414 · Cited by 93 · see citing works

High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment

Naik, B., Gupta, N., Ojha, R., Singh, S., Prajapati, V. K., & Prusty, D. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.05.184 · Cited by 92 · see citing works

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

Mirjalili, V., & Feig, M. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300962x · Cited by 91 · see citing works

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening

Hu, J. S., Liu, Z., Yu, D., & Zhang, Y. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty081 · Cited by 90 · see citing works

Protein Folding Requires Crowd Control in a Simulated Cell

Jefferys, B. R., Kelley, L. A., & Sternberg, M. J. E. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.01.074 · Cited by 89 · see citing works

Bioinformatics and variability in drug response: a protein structural perspective

Lahti, J. L., Tang, G. W., Capriotti, E., Liu, T., & Altman, R. B. (2012) · Journal of The Royal Society Interface · doi:10.1098/rsif.2011.0843 · Cited by 87 · see citing works

Computational protein structure refinement: almost there, yet still so far to go

Feig, M. (2017) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1307 · Cited by 83 · see citing works

An enumerative algorithm for de novo design of proteins with diverse pocket structures

Basanta, B., Bick, M. J., Bera, A. K., Norn, C., Chow, C. M., Carter, L. P., Goreshnik, I., DiMaio, F., & Baker, D. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2005412117 · Cited by 81 · see citing works

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

Zhang, C., Zheng, W., Freddolino, L., & Zhang, Y. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.03.004 · Cited by 80 · see citing works

BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures

Lee, H. S., & Zhang, Y. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23165 · Cited by 80 · see citing works

Molecular Dynamics Simulation Reveals Insights into the Mechanism of Unfolding by the A130T/V Mutations within the MID1 Zinc-Binding Bbox1 Domain

Zhao, Y., Zeng, C., & Massiah, M. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124377 · Cited by 79 · see citing works

ProTSAV: A protein tertiary structure analysis and validation server

Singh, A., Kaushik, R., Mishra, A., Shanker, A., & Jayaram, B. (2015) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2015.10.004 · Cited by 78 · see citing works

Model quality assessment for membrane proteins

Ray, A., Lindahl, E. R., & Wallner, B. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq581 · Cited by 78 · see citing works

Molecular Dynamics Simulation in Drug Discovery: Opportunities and Challenges

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Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction

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A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions

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eFindSite: Enhanced Fingerprint‐Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models

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Physics‐based protein structure refinement in the era of artificial intelligence

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A potential in silico antibody–antigen based diagnostic test for precise identification of Acinetobacter baumannii

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Protein fold recognition using Deep Kernelized Extreme Learning Machine and linear discriminant analysis

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Protein Dynamics in F-like Bacterial Conjugation

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Protein Structure Prediction

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Protein Three-Dimensional Structure Prediction

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Template-Based Protein Structure Prediction

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Accurate protein structure prediction: what comes next?

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Introduction to Protein Structure PredictionPreprint

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