An overview of the prediction of protein DNA-binding sites
Open accessAbstract
Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel prediction methods, increased performance, or practical applications.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Other types of molecules interacting with proteins, as well as protein-protein interactions in membranes, have been studied extensively through the years.
“While other types of molecules interacting with proteins, as well as protein-protein interactions in membranes, have been studied extensively through the years [14–18]”
From Challenges in protein docking (2020) · cites this paper as [15]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
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 · see citing works
Cortes, C., & Vapnik, V. (1995) · Machine Learning · doi:10.1007/bf00994018 · Cited by 59,421 · see citing works
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Cortes, C., & Vapnik, V. N. (1995) · Machine Learning · doi:10.1023/a:1022627411411 · Cited by 34,565 · see citing works
A simple method for displaying the hydropathic character of a protein
Kyte, J., & Doolittle, R. F. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90515-0 · Cited by 22,694 · see citing works
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736 · see citing works
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Šali, A., & Blundell, T. L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1626 · Cited by 12,977 · see citing works
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,994 · see citing works
Protein secondary structure prediction based on position-specific scoring matrices.
Jones, D. C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3091 · Cited by 5,741 · see citing works
CATH – a hierarchic classification of protein domain structures
Orengo, C., Michie, A. D., Jones, S., Jones, D., Swindells, M. B., & Thornton, J. M. (1997) · Structure · doi:10.1016/s0969-2126(97)00260-8 · Cited by 2,608 · see citing works
DNA binding sites: representation and discovery
Stormo, G. D. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.1.16 · Cited by 1,519 · see citing works
DNA sequence-dependent deformability deduced from protein–DNA crystal complexes
Olson, W. K., Gorin, A. A., Lu, X., Hock, L. M., & Zhurkin, V. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.19.11163 · Cited by 1,039 · see citing works
Luscombe, N. M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.13.2860 · Cited by 981 · see citing works
Fauch, E., J-L, S. R., & Pliska (1983) · Chimie thérapeutique · Cited by 699 · see citing works
An overview of the structures of protein-DNA complexes.
Luscombe, N. M., Austin, S. E., Berman, H. M., & Thornton, J. M. (2000) · Genome biology · doi:10.1186/gb-2000-1-1-reviews001 · Cited by 674 · see citing works
Valdar, W. S. J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10146 · Cited by 633 · see citing works
Nagano, N., Orengo, C., & Thornton, J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00649-6 · Cited by 631 · see citing works
A structural taxonomy of DNA-binding domains
Harrison, S. C. (1991) · Nature · doi:10.1038/353715a0 · Cited by 609 · see citing works
Analysis of Catalytic Residues in Enzyme Active Sites
Bartlett, G. J., Porter, C. T., Borkakoti, N., & Thornton, J. M. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01036-7 · Cited by 589 · see citing works
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works
Linden, A. (2006) · Journal of Evaluation in Clinical Practice · doi:10.1111/j.1365-2753.2005.00598.x · Cited by 449 · see citing works
Protein-DNA interactions: a structural analysis
Jones, S., van Heyningen, P., Berman, H. M., & Thornton, J. M. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2659 · Cited by 424 · see citing works
Improving the accuracy of transmembrane protein topology prediction using evolutionary information
Jones, D. T. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl677 · Cited by 420 · see citing works
Wang, L., & Brown, S. J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl298 · Cited by 417 · see citing works
Probabilistic model of the human protein-protein interaction network
Rhodes, D. R., Tomlins, S. A., Varambally, S., Mahavisno, V., Barrette, T. R., Sundaram, S. K., Ghosh, D., Pandey, A., & Chinnaiyan, A. M. (2005) · Nature Biotechnology · doi:10.1038/nbt1103 · Cited by 411 · see citing works
PISCES: recent improvements to a PDB sequence culling server
Wang, G., & Dunbrack, R. L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki402 · Cited by 355 · see citing works
Ahmad, S., Gromiha, M. M., & Sarai, A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg432 · Cited by 345 · see citing works
SMART: identification and annotation of domains from signalling and extracellular protein sequences
Ponting, C. P., Schultz, J., Milpetz, F., & Peer Bork, B. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.229 · Cited by 332 · see citing works
Identification of DNA-binding proteins using support vector machines and evolutionary profiles
Kumar, M., Gromiha, M. M., & Raghava, G. P. S. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-463 · Cited by 279 · see citing works
PSSM-based prediction of DNA binding sites in proteins
Ahmad, S., & Sarai, A. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-33 · Cited by 271 · see citing works
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
Hwang, S., Gou, Z., & Kuznetsov, I. B. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl672 · Cited by 255 · see citing works
A Data Complexity Analysis of Comparative Advantages of Decision Forest Constructors
Ho, T. K. (2002) · Pattern Analysis and Applications · doi:10.1007/s100440200009 · Cited by 214 · see citing works
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
Jones, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg922 · Cited by 204 · see citing works
Lou, W., Wang, X., Chen, F., Chen, Y., Jiang, B., & Zhang, H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086703 · Cited by 197 · see citing works
Annotating Nucleic Acid-Binding Function Based on Protein Structure
Stawiski, E. W., Gregoret, L. M., & Mandel‐Gutfreund, Y. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00031-7 · Cited by 196 · see citing works
Prediction of DNA-binding residues from sequence
Ofran, Y., Mysore, V. P., & Rost, B. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm174 · Cited by 185 · see citing works
Protein-DNA binding specificity predictions with structural models
Morozov, A. V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki875 · Cited by 181 · see citing works
Flexibility analysis of enzyme active sites by crystallographic temperature factors
Yuan, Z., Ju, Z., & Wang, Z. (2003) · Protein Engineering Design and Selection · doi:10.1093/proeng/gzg014 · Cited by 175 · see citing works
Using A Neural Network and Spatial Clustering to Predict the Location of Active Sites in Enzymes
Gutteridge, A., Bartlett, G. J., & Thornton, J. M. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00515-1 · Cited by 175 · see citing works
Efficient Prediction of Nucleic Acid Binding Function from Low-resolution Protein Structures
Szilágyi, A., & Skolnick, J. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.053 · Cited by 166 · see citing works
Using evolutionary and structural information to predict DNA‐binding sites on DNA‐binding proteins
Kuznetsov, I. B., Gou, Z., Li, R., & Hwang, S. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20977 · Cited by 165 · see citing works
Predicting DNA-binding sites of proteins from amino acid sequence
Yan, C., Terribilini, M., Wu, F., Jernigan, R. L., Dobbs, D. L., & Honavar, V. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-262 · Cited by 163 · see citing works
Regulation of transcription: from lambda to eukaryotes
Ptashne, M. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.04.003 · Cited by 158 · see citing works
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
Tjong, H., & Zhou, H. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm008 · Cited by 154 · see citing works
DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions
Gao, M., & Skolnick, J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn332 · Cited by 154 · see citing works
Kernel-based machine learning protocol for predicting DNA-binding proteins
Bhardwaj, N. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki949 · Cited by 153 · see citing works
Wu, J., Liu, H., Duan, X., Ding, Y., Wu, H., Bai, Y., & Sun, X. S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn583 · Cited by 148 · see citing works
Mandel‐Gutfreund, Y., & Margalit, H. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.10.2306 · Cited by 148 · see citing works
Moment-based Prediction of DNA-binding Proteins
Ahmad, S., & Sarai, A. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.05.058 · Cited by 134 · see citing works
Prediction of DNA-binding residues from protein sequence information using random forests
Wang, L., Yang, M. Q., & Yang, J. Y. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-s1-s1 · Cited by 131 · see citing works
LiveBench‐1: Continuous benchmarking of protein structure prediction servers
Bujnicki, J. M., Elofsson, A., Fischer, D., & Rychlewski, L. (2001) · Protein Science · doi:10.1110/ps.40501 · Cited by 130 · see citing works
Ghersi, D., & Sánchez, R. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22154 · Cited by 128 · see citing works
Prediction of protein functional residues from sequence by probability density estimation
Fischer, J. D., Mayer, C., & Söding, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm626 · Cited by 126 · see citing works
Petrova, N. V., & Wu, C. H. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-312 · Cited by 125 · see citing works
TFBSshape: a motif database for DNA shape features of transcription factor binding sites
Yang, L., Zhou, T., Dror, I., Mathelier, A., Wasserman, W. W., Gordân, R., & Rohs, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1087 · Cited by 121 · see citing works
DSSPcont: continuous secondary structure assignments for proteins
Carter, P. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg626 · Cited by 117 · see citing works
Identifying DNA-binding proteins using structural motifs and the electrostatic potential
Shanahan, H. P. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh803 · Cited by 111 · see citing works
PEDANT covers all complete RefSeq genomes
Walter, M. C., Rattei, T., Arnold, R. R., Güldener, U., Münsterkötter, M., Nenova, K., Kastenmüller, G., Tischler, P., Wolling, A., Volz, A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn749 · Cited by 105 · see citing works
Tsuchiya, Y., Kinoshita, K., & Nakamura, H. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20111 · Cited by 97 · see citing works
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction
Si, J.-N., Zhang, Z., Lin, B., Schroeder, M., & Huang, B. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-s1-s7 · Cited by 96 · see citing works
Self-citationGao, M., & Skolnick, J. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000567 · Cited by 89 · see citing works
Ahmad, S., Keskin, Ö., Sarai, A., & Nussinov, R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn573 · Cited by 88 · see citing works
NAPS: a residue-level nucleic acid-binding prediction server
Carson, M. B., Langlois, R. E., & Lu, H. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq361 · Cited by 84 · see citing works
Liu, R., & Hu, J. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24330 · Cited by 84 · see citing works
iDBPs: a web server for the identification of DNA binding proteins
Nimrod, G., Schushan, M., Szilágyi, A., Leslie, C., & Ben‐Tal, N. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq019 · Cited by 82 · see citing works
Karypis, G. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21036 · Cited by 80 · see citing works
Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features
Nimrod, G., Szilágyi, A., Leslie, C. S., & Ben‐Tal, N. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.02.023 · Cited by 78 · see citing works
3D-footprint: a database for the structural analysis of protein–DNA complexes
Contreras‐Moreira, B. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp781 · Cited by 73 · see citing works
Predicting DNA- and RNA-binding proteins from sequences with kernel methods
Shao, X., Tian, Y., Wu, L., Wang, Y., Jing, L., & Deng, N.-Y. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.01.024 · Cited by 70 · see citing works
Ma, X., Guo, J., Liu, H., Xie, J., & Sun, X. S. (2012) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2012.106 · Cited by 68 · see citing works
Identifying splicing sites in eukaryotic RNA: support vector machine approach
Sun, Y.-F., Fan, X., & Li, Y. (2002) · Computers in Biology and Medicine · doi:10.1016/s0010-4825(02)00057-4 · Cited by 67 · see citing works
Using structural motif templates to identify proteins with DNA binding function
Jones, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg386 · Cited by 64 · see citing works
The Protein-DNA Interface database
Norambuena, T., & Melo, F. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-262 · Cited by 62 · see citing works
Using protein binding site prediction to improve protein docking
Huang, B., & Schroeder, M. (2008) · Gene · doi:10.1016/j.gene.2008.06.014 · Cited by 59 · see citing works
Shazman, S., Celniker, G., Haber, O., Glaser, F., & Mandel‐Gutfreund, Y. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm401 · Cited by 58 · see citing works
A novel computational method to predict transcription factor DNA binding preference
Qian, Z., Cai, Y., & Li, Y. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.07.149 · Cited by 57 · see citing works
Chu, W.-Y., Huang, Y., Huang, C.-C., Cheng, Y., Huang, C., & Oyang, Y.-J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp449 · Cited by 55 · see citing works
Özbek, P., Soner, S., Erman, B., & Haliloǧlu, T. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq396 · Cited by 55 · see citing works
Chen, Y. C., Wright, J. D., & Lim, C. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks481 · Cited by 54 · see citing works
Extracting Sequence Features to Predict\nProtein–DNA Interactions: A Comparative Study
Zhou, Q., & Liu, J. S. (2008) · Digital Access to Scholarship at Harvard (DASH) (Harvard University) · Cited by 52 · see citing works
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces
Tsuchiya, Y., Kinoshita, K., & Nakamura, H. (2004) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti232 · Cited by 51 · see citing works
Protein tertiary structure prediction using a branch and bound algorithm
Eyrich, V. A., Standley, D. M., Felts, A. K., & Friesner, R. A. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990401)35:1 · Cited by 50 · see citing works
Li, T., Li, Q., Liu, S., Fan, G.-L., Zuo, Y., & Peng, Y. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt029 · Cited by 47 · see citing works
Improving the accuracy of predicting disulfide connectivity by feature selection
Zhu, L., Yang, J., Song, J., Chou, K., & Shen, H. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21433 · Cited by 43 · see citing works
Wang, K., Horst, J. A., Cheng, G., Nickle, D. C., & Samudrala, R. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000181 · Cited by 39 · see citing works
A Novel Computational Approach To Predict Transcription Factor DNA Binding Preference
Cai, Y., He, J., Li, X., Lü, L., Yang, X., Feng, K., Lu, W., & Kong, X. (2008) · Journal of Proteome Research · doi:10.1021/pr800717y · Cited by 38 · see citing works
An improved prediction of catalytic residues in enzyme structures
Tang, Y. R., Sheng, Z.-Y., Chen, Y., & Zhang, Z. (2008) · Protein Engineering Design and Selection · doi:10.1093/protein/gzn003 · Cited by 38 · see citing works
Xiong, Y., Xia, J., Zhang, W., & Liu, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028440 · Cited by 33 · see citing works
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif
Ferrer‐Costa, C., Shanahan, H. P., Jones, S., & Thornton, J. M. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti575 · Cited by 30 · see citing works
Zhang, Y., Xu, J., Zheng, W. H., Zhang, C., Qiu, X., Chen, K., & Ruan, J. (2014) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2014.09.002 · Cited by 29 · see citing works
Computational Prediction of DNA-Protein Interactions: A Review
Ding, X.-M., Pan, X., Chen, X., & Shen, H. (2010) · Current Computer - Aided Drug Design · doi:10.2174/157340910791760091 · Cited by 28 · see citing works
Predicting DNA-binding sites of proteins based on sequential and 3D structural information
Li, B., Feng, K., Ding, J., & Cai, Y. (2014) · Molecular Genetics and Genomics · doi:10.1007/s00438-014-0812-x · Cited by 23 · see citing works
Structure Based Prediction of Binding Residues on DNA-binding Proteins
Bhardwaj, N., Langlois, R. E., Zhao, G., & Lu, H. J. (2005) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/iembs.2005.1617004 · Cited by 23 · see citing works
Qian, Z., Lu, L., Liu, X., Cai, Y., & Li, Y. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm348 · Cited by 18 · see citing works
Identification of DNA-Binding Proteins Using Support Vector Machine with Sequence Information
Ma, X., Wu, J., & Xue, X. (2013) · Computational and Mathematical Methods in Medicine · doi:10.1155/2013/524502 · Cited by 17 · see citing works
Structure-Based DNA-Binding Prediction and Design
Alibés, A., Serrano, L. G., & Nadra, A. D. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-753-2_4 · Cited by 16 · see citing works
Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors
Schröder, A., Eichner, J., Supper, J., Eichner, J., Wanke, D., Henneges, C., & Zell, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013876 · Cited by 15 · see citing works
IMPROVING HOMOLOGY MODELS FOR PROTEIN-LIGAND BINDING SITES
Kauffman, C., Rangwala, H., & Karypis, G. (2008) · IEEE Computational Systems Bioinformatics Conference (CSB) · doi:10.1142/9781848162648_0019 · Cited by 11 · see citing works
AN ANALYSIS OF INFORMATION CONTENT PRESENT IN PROTEIN-DNA INTERACTIONS
Kauffman, C., & Karypis, G. (2007) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812776136_0046 · Cited by 11 · see citing works
Predicting experimental properties of integral membrane proteins by a naive Bayes approach
Martín-Galiano, A. J., Smialowski, P., & Frishman, D. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21605 · Cited by 8 · see citing works
Computational Methods for DNA-binding Protein and Binding Residue Prediction
Lu, Y., Wang, X., Chen, X., & Zhao, G. (2013) · Protein and Peptide Letters · doi:10.2174/0929866511320030013 · Cited by 5 · see citing works
An Overview of the De Novo Prediction of Enzyme Catalytic Residues (Supplementry file)
Zhang, Z., Tang, Y., Sheng, Z.-Y., & Zhao, D. (2009) · Current Bioinformatics · doi:10.2174/157489309789071110 · Cited by 4 · see citing works
Extracting sequence features to predict protein–DNA interactions: a comparative study
Zhou, Q., & Liu, J. S. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn361 · Cited by 2 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Qiu, J., Bernhofer, M., Heinzinger, M., Kemper, S., Norambuena, T., Melo, F., & Rost, B. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.02.026 · Cited by 123 · see citing works
Zhang, J., Ma, Z., & Kurgan, L. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx168 · Cited by 120 · see citing works
Hu, J. S., Li, Y., Zhang, M., Yang, X., Shen, H., & Yu, D. (2016) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2016.2616469 · Cited by 103 · see citing works
A Review of DNA-binding Proteins Prediction Methods
Qu, K., Wei, L., & Zou, Q. (2018) · Current Bioinformatics · doi:10.2174/1574893614666181212102030 · Cited by 98 · see citing works
Zhu, Y., Hu, J. S., Song, X., & Yu, D. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00749 · Cited by 93 · see citing works
Computational Prediction of RNA-Binding Proteins and Binding Sites
Si, J.-N., Cui, J. H., Cheng, J. Q., & Wu, R. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms161125952 · Cited by 80 · see citing works
Self-citationDescribePROT: database of amino acid-level protein structure and function predictions
Zhao, B., Katuwawala, A., Oldfield, C. J., Dunker, A. K., Faraggi, E., Gsponer, J. A., Kloczkowski, A., Malhis, N., Mirdita, M., Zoran Obradovic, A., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa931 · Cited by 76 · see citing works
Vakser, I. A. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.07.001 · Cited by 62 · see citing works
Cogill, S., & Wang, L. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw498 · Cited by 58 · see citing works
iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks
Nguyen, B. P., Nguyen, Q. H., Doan-Ngoc, G., Nguyen‐Vo, T., & Rahardja, S. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3295-2 · Cited by 54 · see citing works
Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps
Amirkhani, A., Kolahdoozi, M., Wang, C., & Kurgan, L. (2018) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2018.2890261 · Cited by 41 · see citing works
Computational prediction of functions of intrinsically disordered regions
Katuwawala, A., Ghadermarzi, S., & Kurgan, L. (2019) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2019.04.006 · Cited by 38 · see citing works
Zhang, Y., Qiao, S., Ji, S., Han, N., Liu, D., & Zhou, J. (2019) · Engineering Applications of Artificial Intelligence · doi:10.1016/j.engappai.2019.01.003 · Cited by 37 · see citing works
PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity
Yang, W., & Deng, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-57778-1 · Cited by 37 · see citing works
DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences
Zhang, J., Ghadermarzi, S., Katuwawala, A., & Kurgan, L. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab336 · Cited by 37 · see citing works
Shen, C., Ding, Y., Tang, J., Song, J. G., & Guo, F. (2017) · Molecules · doi:10.3390/molecules22122079 · Cited by 36 · see citing works
A deep learning-based method for the prediction of DNA interacting residues in a protein
Patiyal, S., Dhall, A., & Raghava, G. P. S. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac322 · Cited by 38 · see citing works
Zhang, J., Basu, S., & Kurgan, L. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1131 · Cited by 35 · see citing works
Wu, Y., Xie, L., Jiang, Y., & Li, T. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.02.133 · Cited by 35 · see citing works
Hassan, S., Berk, K., & Aronsson, H. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1894980 · Cited by 34 · see citing works
Delgado, J., Radusky, L., Climente-González, H., & Serrano, L. G. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky228 · Cited by 31 · see citing works
Harini, K., Kihara, D., & Gromiha, M. M. (2023) · Methods · doi:10.1016/j.ymeth.2023.03.002 · Cited by 30 · see citing works
Genome-wide systematic identification of methyltransferase recognition and modification patterns
Jensen, T. Ø., Tellgren‐Roth, C., Redl, S., Maury, J., Jacobsen, S. A. B., Pedersen, L. E., & Nielsen, A. T. (2019) · Nature Communications · doi:10.1038/s41467-019-11179-9 · Cited by 27 · see citing works
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case
Peled, S., Leiderman, O., Charar, R., Efroni, G., Shav‐Tal, Y., & Ofran, Y. (2016) · Nature Communications · doi:10.1038/ncomms13424 · Cited by 26 · see citing works
Structure-based prediction of protein-nucleic acid binding using graph neural networks
Sagendorf, J. M., Mitra, R., Huang, J., Chen, X. S., & Rohs, R. (2024) · Biophysical Reviews · doi:10.1007/s12551-024-01201-w · Cited by 25 · see citing works
Diez, C., Juncos, M. J., Dujovne, M. V., & Capdevila, D. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042179 · Cited by 23 · see citing works
Wieczór, M., & Czub, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx534 · Cited by 23 · see citing works
Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature
Hu, J. S., Bai, Y., Zheng, L., Jia, N.-X., Yu, D., & Zhang, G. (2021) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2021.3123828 · Cited by 22 · see citing works
Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma
Tetz, V., & Tetz, G. V. (2019) · Scientific Reports · doi:10.1038/s41598-019-54618-9 · Cited by 21 · see citing works
Jiang, C., Lv, W., & Li, J. (2023) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2023.3238001 · Cited by 21 · see citing works
Zhao, Y., Piao, Y. Z., Zhang, C., Jiang, Y., Liu, A., Cui, S., Zhi, D., Zhen, Y., & Zhang, S. (2017) · Journal of Materials Chemistry B · doi:10.1039/c7tb01915g · Cited by 21 · see citing works
Zhou, C., Zhang, H., Fang, H., Sun, Y., Zhou, H., Yang, G., & Fuping, L. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.11.028 · Cited by 20 · see citing works
Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins
Srivastava, A., Ahmad, S., & Gromiha, M. M. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19061595 · Cited by 19 · see citing works
DNA–protein interaction: identification, prediction and data analysis
Emamjomeh, A., Choobineh, D., Hajieghrari, B., Mahdinezhad, N., & Khodavirdipour, A. (2019) · Molecular Biology Reports · doi:10.1007/s11033-019-04763-1 · Cited by 19 · see citing works
An Efficient Deep Learning Approach for DNA-Binding Proteins Classification from Primary Sequences
Ahmed, N. Y., Alsanousi, W. A., Hamid, E. M., Elbashir, M. K., Alaidarous, K. M., Mohammed, M. A. Y., & Musa, M. E. M. (2024) · International Journal of Computational Intelligence Systems · doi:10.1007/s44196-024-00462-3 · Cited by 18 · see citing works
Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles
Sharma, R., Kumar, S., Tsunoda, T., Kumarevel, T., & Sharma, A. K. (2020) · Analytical Biochemistry · doi:10.1016/j.ab.2020.113954 · Cited by 17 · see citing works
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences
Basu, S., Jing, Y., Kihara, D., & Kurgan, L. (2024) · Briefings Bioinform. · doi:10.1093/bib/bbaf016 · Cited by 15 · see citing works
Non-H3 CDR template selection in antibody modeling through machine learning
Long, X., Jeliazkov, J. R., & Gray, J. J. (2019) · PeerJ · doi:10.7717/peerj.6179 · Cited by 14 · see citing works
DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method
Hendrix, S. G., Chang, K. Y., Ryu, Z., & Xie, Z. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115510 · Cited by 14 · see citing works
Song, J., & Kurgan, L. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad184 · Cited by 13 · see citing works
Pandey, P., Hasnain, S., & Ahmad, S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20217-3 · Cited by 13 · see citing works
Dissecting and analyzing key residues in protein‐DNA complexes
Kulandaisamy, A., Srivastava, A., Nagarajan, R., & Gromiha, M. M. (2017) · Journal of Molecular Recognition · doi:10.1002/jmr.2692 · Cited by 12 · see citing works
Tahmid, M. T., Hasan, A. K. M. M., & Bayzid, M. S. (2025) · Communications Biology · doi:10.1038/s42003-025-07534-w · Cited by 11 · see citing works
Mass Spectrometry for Assessing Protein–Nucleic Acid Interactions
He, X.-M., Chen, X., & Wang, Y.-S. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c04353 · Cited by 10 · see citing works
An evolution-based DNA-binding residue predictor using a dynamic query-driven learning scheme
Chai, H., Zhang, J., Yang, G., & Ma, Z. (2016) · Molecular BioSystems · doi:10.1039/c6mb00626d · Cited by 11 · see citing works
Mayer, C., Vogt, A., Uslu, T., Scalzitti, N., Chennen, K., Poch, O., & Thompson, J. (2023) · Journal of Fungi · doi:10.3390/jof9040424 · Cited by 10 · see citing works
Gupta, S., Jyoti, Bhati, U., Kesarwani, V., Sharma, A., & Shankar, R. (2025) · Plant Communications · doi:10.1016/j.xplc.2025.101543 · Cited by 10 · see citing works
Corral-Corral, R., Beltrán, J., Brizuela, C. A., & del Rio, G. (2017) · Molecules · doi:10.3390/molecules22101673 · Cited by 10 · see citing works
An Overview of the Protein Thermostability Prediction: Databases and Tools
Zahiri, J. (2016) · Journal of Nanomedicine Research · doi:10.15406/jnmr.2016.03.00072 · Cited by 10 · see citing works
Deep Learning‐Based Classification of Histone–DNA Interactions Using Drying Droplet Patterns
Vaez, S., Dadfar, B., Koenig, M., Franzreb, M., & Lahann, J. (2024) · Small Science · doi:10.1002/smsc.202400252 · Cited by 9 · see citing works
Roy, A., & Ray, S. (2023) · Molecular Biotechnology · doi:10.1007/s12033-023-00711-4 · Cited by 9 · see citing works
Murad, T., Chourasia, P., Ali, S., & Patterson, M. (2025) · Communications in computer and information science · doi:10.1007/978-981-96-6960-8_25 · Cited by 7 · see citing works
A Survey of Deep Learning Methods and Tools for Protein Binding Site Prediction
Rohulia, A., Wang, Y., & Cheng, J. J. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4662-5_5 · Cited by 7 · see citing works
ENSEMBLE-CNN: Predicting DNA Binding Sites in Protein Sequences by an Ensemble Deep Learning Method
Zhang, Y., Qiao, S., Ji, S., & Zhou, J. (2018) · Lecture notes in computer science · doi:10.1007/978-3-319-95933-7_37 · Cited by 7 · see citing works
Towards a Shared, Conceptual Model-Based Understanding of Proteins and Their Interactions
Palacio, A. L., & Pastor, Ó. (2021) · IEEE Access · doi:10.1109/access.2021.3080040 · Cited by 7 · see citing works
Liu, S., Gomez-Alcala, P., Leemans, C., Glassford, W. J., Melo, L. A. N., Lu, X., Mann, R. S., & Bussemaker, H. J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf831 · Cited by 7 · see citing works
Wu, Z., Basu, S., Wu, X., & Kurgan, L. (2022) · Protein Science · doi:10.1002/pro.4544 · Cited by 6 · see citing works
Insights from Ion Binding Site Network Analysis into Evolution and Functions of Proteins
Škrlj, B., Kunej, T., & Konc, J. (2018) · Molecular Informatics · doi:10.1002/minf.201700144 · Cited by 6 · see citing works
Protein Analysis: From Sequence to Structure
Jani, J., & Pappachan, A. (2021) · Springer eBooks · doi:10.1007/978-981-33-6191-1_4 · Cited by 5 · see citing works
A comprehensive review of computational methods for Protein-DNA binding site prediction
Liu, Z., Qiu, W., Liu, Y., He, Y., Pei, W., Zhu, Y.-H., & Qiu, J. (2025) · Analytical Biochemistry · doi:10.1016/j.ab.2025.115862 · Cited by 5 · see citing works
DescribePROT Database of Residue-Level Protein Structure and Function Annotations
Zhao, B., Basu, S., & Kurgan, L. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4196-5_10 · Cited by 4 · see citing works
Basu, S., Yang, Y., & Kurgan, L. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103085 · Cited by 4 · see citing works
Yadav, D., Kaur, S., Banerjee, D., & Bhattacharyya, R. (2020) · Biotechnology and Applied Biochemistry · doi:10.1002/bab.2052 · Cited by 4 · see citing works
Zhu, F., & Zhao, Q. (2024) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2024.136615 · Cited by 4 · see citing works
Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces
Mukherjee, S., & Nithin, C. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90264-9.00011-8 · Cited by 5 · see citing works
ProGraphTrans: multimodal dynamic collaborative framework for protein representation learning
Li, Z., Liu, Y., Han, G., Yu, Z.-G., & Liu, Y. (2025) · BMC Biology · doi:10.1186/s12915-025-02432-3 · Cited by 3 · see citing works
Wu, Y. J., Zhan, H., Zhang, S., Wang, C., Zhang, M., Wang, M., Tian, B., Yang, Q., Jia, R., Chen, S., et al. (2025) · The FASEB Journal · doi:10.1096/fj.202402555rr · Cited by 3 · see citing works
Protein Stability Determination (PSD): A Tool for Proteomics Analysis
Panja, A. S., Nag, A., Bandopadhyay, B., & Maiti, S. (2018) · Current Bioinformatics · doi:10.2174/1574893613666180315121614 · Cited by 3 · see citing works
InPrNa: A Tool for Insight Into Protein–Nucleic Acids Interaction Information
Wang, W., Zhao, Y., Zhang, H., Zhang, S., Li, K., & Lv, H. (2019) · IEEE Access · doi:10.1109/access.2019.2943748 · Cited by 3 · see citing works
Nitrile-Imine-Mediated Cross-Linking of Peptides to Oligonucleotides in Gas-Phase Ion Complexes
Wan, J., Vlk, M., Wei, C., & Tureček, F. (2025) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.5c00100 · Cited by 2 · see citing works
Wu, C., Zhang, F., Jia, P., Zhu, J., Zeng, M., Hu, G., Wang, K., Kurgan, L., & Li, M. (2026) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzag032 · Cited by 2 · see citing works
A new, harmless, high-throughput endosperm-based DNA extraction method for wheat
Ma, Z., Wang, Y., Wei, W., & Ru, Z. (2019) · Ciência Rural · doi:10.1590/0103-8478cr20170936 · Cited by 2 · see citing works
Complementarity of the residue-level protein function and structure predictions in human proteins
Biró, B., Zhao, B., & Kurgan, L. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.003 · Cited by 2 · see citing works
Zhao, H., Zhu, B., Jiang, T., Cui, Z., & Wu, H. (2023) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2024008 · Cited by 1 · see citing works
Advances in Language-Model-Informed Protein–Nucleic Acid Binding Site Prediction
Tarafder, S., Wang, X., Roche, R., & Bhattacharya, D. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4623-6_9 · Cited by 1 · see citing works
An extension of fuzzy topological approach for comparison of genetic sequences
Georgiou, D. N., Karakasidis, T. E., Megaritis, A. C., Nieto, J. J., & Torres, Á. (2015) · Journal of Intelligent & Fuzzy Systems · doi:10.3233/ifs-151701 · Cited by 1 · see citing works
Olivares‐Quiroz, L. (2016) · European Biophysics Journal · doi:10.1007/s00249-015-1108-8 · Cited by 1 · see citing works
Hu, J. S., Liu, Z., & Yu, D.-J. (2017) · Asian Conference on Pattern Recognition · doi:10.1109/acpr.2017.9 · Cited by 1 · see citing works
Protein-DNA complexation: contact profiles in DNA grooves
Zhitnikova, M. Y., & Shestopalova, A. V. (2017) · Biophysical Bulletin · doi:10.26565/2075-3810-2017-38-06 · Cited by 1 · see citing works
Sequence Based DNA-Binding Protein Prediction
Farisa, T. S., & Isaac, D. E. (2021) · International Journal of Recent Technology and Engineering (IJRTE) · doi:10.35940/ijrte.b3665.039621
IProDNA-CapsNet: Identifying protein-DNA binding residues using capsule neural networks
Nguyen, B. P., Nguyen, Q., Doan-Ngoc, G., Nguyen‐Vo, T., & Rahardja, S. (2021) · doi:10.26686/wgtn.14315873.v1
IProDNA-CapsNet: Identifying protein-DNA binding residues using capsule neural networks
Nguyen, B. P., Nguyen, Q., Doan-Ngoc, G., Nguyen‐Vo, T., & Rahardja, S. (2021) · doi:10.26686/wgtn.14315873
Zhitnikova, M. Y., & Shestopalova, A. V. (2023) · Biophysical Bulletin · doi:10.26565/2075-3810-2022-48-02
Current Progress in Gene and Genome Annotation
Alam, S., Israr, J., & Kumar, A. (2024) · Springer eBooks · doi:10.1007/978-981-97-3169-5_3
Emerging Topics in Protein-DNA Interactions
Mirza, S., Pandey, P., Hasnain, S., & Ahmad, S. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00140-8
Landeros-Sánchez, B., Dueñas-Mena, D. L., Gutierrez-Pabello, J. A., Quintero-Chávez, K., Perea, M. D. C. B., Padilla, D. M. D., Hernández, O. C., Chávez-Méndez, J. R., Zacarias, J. M. A., & Sancho, G. B. V. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252312687
Unravelling Protein-DNA Interaction Predictions: A State-of-the-Art review
Thomas, N., & Sophia, P. E. (2025) · International Conference on Trends in Engineering Systems and Technologies (ICTEST) · doi:10.1109/ictest64710.2025.11042871
PRIMED: predicting DNA binding residues by leveraging pre-trained protein language models
Zhang, L., Li, X., Song, R., Song, Q., & Fan, X. (2026) · Frontiers in Artificial Intelligence · doi:10.3389/frai.2026.1763313
Liu, Z., & Zhang, R. (2026) · Molecular Diversity · doi:10.1007/s11030-026-11557-8
Insights into the nicotine bioremediation potential of bacteria isolated from tobacco field soil
Siddiqui, B. N., Muccee, F., Haddad, A. H. I. A., Hussain, N., & Raza, A. (2026) · Biologia · doi:10.1007/s11756-026-02235-z
- Authors
- Si, J., Zhao, R., & Wu, R.
- Affiliations
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Beijing Forestry University (CN)
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2015-03-06
- Volume
- 16
- Issue
- 3
- Pages
- 5194-5215
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC4394471
- OpenAlex
- W1977628834
- Cited by
- 91
- References
- 102
- Citations by year
- 2026: 4 · 2025: 12 · 2024: 9 · 2023: 9 · 2022: 6 · 2021: 10 · 2020: 7 · 2019: 10 · 2018: 8 · 2017: 8 · 2016: 6 · 2015: 2
- FWCI
- 0.78
- Type
- journal article
- Language
- en
- Open access
- gold
- dx.doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Natural Science Foundation of China
- Northeast Forestry University
- Beijing Forestry University
- Fundamental Research Funds for the Central Universities (31401138, TD2012–04)
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-DNA binding sites, DNA binding site prediction, sequence-based prediction, structure-based prediction, homology modeling, threading, machine learning, protein-DNA interactions
- MeSH terms
- Algorithms, Animals, Artificial Intelligence, Binding Sites, DNA, DNA-Binding Proteins, Humans, Protein Binding, Computational Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review