Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes

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

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Genheden, S., & Ryde, U. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1032936 · Cited by 5,636 · see citing works

The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution

Ban, N., Nissen, P., Hansen, J., Moore, P. B., & Steitz, T. A. (2000) · Science · doi:10.1126/science.289.5481.905 · Cited by 3,327 · see citing works

HADDOCK:  A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187 · see citing works

PatchDock and SymmDock: servers for rigid and symmetric docking

Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018 · see citing works

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.09.014 · Cited by 2,785 · see citing works

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2012) · Nature Methods · doi:10.1038/nmeth.1818 · Cited by 2,288 · see citing works

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B. M., Strein, C., Davey, N. E., Humphreys, D. T., Preiss, T., Steinmetz, L. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.031 · Cited by 2,132 · see citing works

A census of human RNA-binding proteins

Gerstberger, S., Hafner, M., & Tuschl, T. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3813 · Cited by 2,032 · see citing works

ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers

Pierce, B. G., Wiehe, K. J., Hwang, H., Kim, B., Vreven, T., & Weng, Z. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu097 · Cited by 1,767 · see citing works

Software for molecular docking: a review

Pagadala, N. S., Syed, K., & Tuszynski, J. (2017) · Biophysical Reviews · doi:10.1007/s12551-016-0247-1 · Cited by 1,522 · see citing works

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Yan, Y., Zhang, D., Zhou, P., Li, B., & Huang, S. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx407 · Cited by 1,479 · see citing works

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

Johnson, J. M., Castle, J. C., Garrett-Engele, P. W., Kan, Z., Loerch, P., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R. B., & Shoemaker, D. D. (2003) · Science · doi:10.1126/science.1090100 · Cited by 1,418 · see citing works

RNA‐binding proteins and post‐transcriptional gene regulation

Glisovic, T., Bachorik, J. L., Yong, J., & Dreyfuss, G. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.03.004 · Cited by 1,398 · see citing works

The rise of regulatory RNA

Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,389 · see citing works

RNA-binding proteins: modular design for efficient function

Lunde, B. M., Moore, C. L., & Varani, G. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2178 · Cited by 1,322 · see citing works

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

Baltz, A. G., Munschauer, M., Schwanhäußer, B., Vasile, A. I., Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.021 · Cited by 1,175 · see citing works

RNA-binding proteins in human genetic disease

Gebauer, F., Schwarzl, T., Valcárcel, J., & Hentze, M. W. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00302-y · Cited by 1,174 · see citing works

RNA and Disease

Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,152 · see citing works

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A., Aflalo, C., & Vakser, I. (1992) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.89.6.2195 · Cited by 1,143 · see citing works

The RNA recognition motif, a plastic RNA‐binding platform to regulate post‐transcriptional gene expression

Maris, C., Dominguez, C., & Allain, F. H. ‐. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04653.x · Cited by 1,135 · see citing works

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

Zhou, H., & Zhou, Y. (2002) · Protein Science · doi:10.1110/ps.0217002 · Cited by 902 · cited 1× · see citing works

PIPER: An FFT‐based protein docking program with pairwise potentials

Kozakov, D., Brenke, R., Comeau, S. R., & Vajda, S. (2006) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21117 · Cited by 865 · see citing works

ClusPro: a fully automated algorithm for protein-protein docking

Comeau, S. R., GATCHELL, D. W., Vajda, S., & Camacho, C. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh354 · Cited by 826 · see citing works

GRAMM-X public web server for protein-protein docking

Tovchigrechko, A., & Vakser, I. A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl206 · Cited by 807 · see citing works

RNA processing and its regulation: global insights into biological networks

Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 760 · see citing works

CAPRI: A Critical Assessment of PRedicted Interactions

Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703 · see citing works

HexServer: an FFT-based protein docking server powered by graphics processors

Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M., & Ritchie, D. W. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq311 · Cited by 674 · see citing works

RNA-binding proteins in human genetic disease

Lukong, K. E., Chang, K.-W., Khandjian, E. W., & Richard, S. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.05.004 · Cited by 649 · see citing works

RBPDB: a database of RNA-binding specificities

Cook, K. B., Kazan, H., Zuberi, K., Morris, Q., & Hughes, T. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1069 · Cited by 638 · see citing works

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 584 · see citing works

A large‐scale experiment to assess protein structure prediction methods

Moult, J., Pedersen, J. T., Judson, R., & Fidelis, K. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340230303 · Cited by 555 · see citing works

The pre-mRNA binding K protein contains a novel evolutionary conserved motif

Siomi, H., Matunis, M. J., Michael, W. M., & Dreyfuss, G. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.5.1193 · Cited by 533 · see citing works

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

Russel, D., Lasker, K., Webb, B., Velázquez-Muriel, J. A., Tjioe, E., Schneidman‐Duhovny, D., Peterson, B. E., & Šali, A. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001244 · Cited by 509 · see citing works

RIBOSOMAL RNA AND TRANSLATION

Noller, H. F. (1991) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.60.070191.001203 · Cited by 496 · see citing works

Molecular basis of double‐stranded RNA‐protein interactions: structure of a dsRNA‐binding domain complexed with dsRNA

Ryter, J. M., & Schultz, S. C. (1998) · The EMBO Journal · doi:10.1093/emboj/17.24.7505 · Cited by 479 · see citing works

A structural understanding of the dynamic ribosome machine

Steitz, T. A. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2352 · Cited by 449 · see citing works

Messenger RNA Splicing in Yeast: Clues to Why the Spliceosome Is a Ribonucleoprotein

Guthrie, C. (1991) · Science · doi:10.1126/science.1853200 · Cited by 430 · see citing works

GeneSilico protein structure prediction meta-server

Kurowski, M. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg557 · Cited by 407 · see citing works

Critical assessment of methods of protein structure prediction (CASP)—Round XII

Moult, J., Fidelis, K. A., Kryshtafovych, A., Schwede, T. F., & Tramontano, A. L. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25415 · Cited by 327 · see citing works

pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

Jiménez‐García, B., Pons, C., & Fernández‐Recio, J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt262 · Cited by 318 · see citing works

Protein-Protein Docking: From Interaction to Interactome

Vakser, I. A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.08.033 · Cited by 318 · see citing works

Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins

Castelló, A., Hentze, M. W., & Preiß, T. (2015) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2015.09.012 · Cited by 274 · see citing works

Docking, scoring, and affinity prediction in CAPRI

Lensink, M. F., & Wodak, S. J. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24428 · Cited by 249 · see citing works

NPDock: a web server for protein–nucleic acid docking

Tuszyńska, I., Magnus, M., Jonak, K., Dawson, W., & Bujnicki, J. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv493 · Cited by 241 · see citing works

Knowledge-Based Protein Modeling

Johnson, M. S., Srinivasan, N., Sowdhamini, R., & Blundell, T. L. (1994) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239409086797 · Cited by 234 · see citing works

Docking and scoring protein interactions: CAPRI 2009

Lensink, M. F., & Wodak, S. J. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22818 · Cited by 226 · see citing works

The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities.

Burd, C. G., Matunis, E. L., & Dreyfuss, G. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.7.3419 · Cited by 222 · see citing works

Crystal structure of a zinc-finger–RNA complex reveals two modes of molecular recognition

Lü, D., Searles, M. A., & Klug, A. (2003) · Nature · doi:10.1038/nature02088 · Cited by 203 · see citing works

Ab initio protein structure prediction

Hardin, C., Pogorelov, T. V., & Luthey-Schulten, Z. A. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00306-8 · Cited by 197 · see citing works

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

Huang, S.-Y., & Zou, X. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku077 · Cited by 192 · see citing works

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao, Z., Adamiak, R. W., Antczak, M., Batey, R., Becka, A. J., Biesiada, M., Boniecki, M., Bujnicki, J. M., Chen, S., Cheng, C. Y., et al. (2017) · RNA · doi:10.1261/rna.060368.116 · Cited by 189 · see citing works

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

van Dijk, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl412 · Cited by 187 · see citing works

RNA Structure: Advances and Assessment of 3D Structure Prediction

Miao, Z., & Westhof, É. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-034125 · Cited by 186 · see citing works

7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription

Peterlin, B. M., Brogie, J. E., & Price, D. H. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.106 · Cited by 181 · see citing works

Templates are available to model nearly all complexes of structurally characterized proteins

Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200678109 · Cited by 179 · see citing works

mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription

Minvielle-Sébastia, L., & Keller, W. D. (1999) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(99)80049-0 · Cited by 178 · see citing works

Crystallization of RNA and RNA?protein complexes

Ke, A. (2004) · Methods · doi:10.1016/j.ymeth.2004.03.027 · Cited by 171 · see citing works

The structure of the box C/D enzyme reveals regulation of RNA methylation

Lapinaitė, A., Simon, B., Skjærven, L., Rakwalska‐Bange, M., Gabel, F., & Carlomagno, T. (2013) · Nature · doi:10.1038/nature12581 · Cited by 170 · see citing works

Statistical analysis of atomic contacts at RNA–protein interfaces

Treger, M., & Westhof, É. (2001) · Journal of Molecular Recognition · doi:10.1002/jmr.534 · Cited by 170 · see citing works

ADAR Gene Family and A-to-I RNA Editing: Diverse Roles in Posttranscriptional Gene Regulation

Valente, L., & Nishikura, K. (2005) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(04)79006-6 · Cited by 168 · see citing works

Protein families and RNA recognition

Chen, Y., & Varani, G. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04650.x · Cited by 163 · see citing works

RNA Structure Prediction: An Overview of Methods

Seetin, M. G., & Mathews, D. H. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-949-5_8 · Cited by 159 · see citing works

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

Cruz, J. A., Blanchet, M.-F., Boniecki, M. J., Bujnicki, J. M., Chen, S.-J., Cao, S., Das, R., Ding, F., Dokholyan, N., Flores, S., et al. (2012) · RNA: A publication of the RNA Society · doi:10.1261/rna.031054.111 · Cited by 157 · see citing works

Accounting for conformational changes during protein–protein docking

Zacharias, M. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.02.001 · Cited by 151 · see citing works

Developments in X-ray Crystallographic Structure Determination of Biological Macromolecules

Garman, E. F. (2014) · Science · doi:10.1126/science.1247829 · Cited by 148 · see citing works

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

Liao, Y., Castelló, A., Fischer, B., Leicht, S., Föehr, S., Frese, C. K., Ragan, C., Kurscheid, S., Pagler, E., Hao, Y., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.06.084 · Cited by 141 · see citing works

Multiscale Modeling of Proteins

Tozzini, V. (2009) · Accounts of Chemical Research · doi:10.1021/ar9001476 · Cited by 140 · see citing works

5′ exon interactions within the human spliceosome establish a framework for exon junction complex structure and assemblyPreprint

Reichert, V. L., Hir, H. L., Jurica, M. S., & Moore, M. J. (2002) · Genes & Development · doi:10.1101/gad.1030602 · Cited by 131 · see citing works

Serial interactome capture of the human cell nucleus

Conrad, T., Albrecht, A.-S., Costa, V. R. D. M., Sauer, S., Meierhofer, D., & Ørom, U. A. (2016) · Nature Communications · doi:10.1038/ncomms11212 · Cited by 130 · see citing works

Protein–protein docking dealing with the unknown

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21276 · Cited by 128 · see citing works

mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions

Pires, D. E. V., & Ascher, D. B. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx236 · Cited by 127 · see citing works

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

Tuszyńska, I., & Bujnicki, J. M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-348 · Cited by 125 · see citing works

A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues

Yan, J. R., Friedrich, S., & Kurgan, L. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv023 · Cited by 118 · see citing works

EPR-aided approach for solution structure determination of large RNAs or protein–RNA complexes

Duss, O., Yulikov, M., Jeschke, G., & Allain, F. H. ‐. (2014) · Nature Communications · doi:10.1038/ncomms4669 · Cited by 114 · see citing works

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

Zhao, H., Yang, Y., & Zhou, Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1266 · Cited by 112 · see citing works

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation

Śmietański, M., Werner, M., Purta, E., Kaminska, K. H., Stȩpiński, J., Darżynkiewicz, E., Nowotny, M., & Bujnicki, J. M. (2014) · Nature Communications · doi:10.1038/ncomms4004 · Cited by 104 · see citing works

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

de Vries, S. J., Schindler, C., de Beauchêne, I. C., & Zacharias, M. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2014.12.015 · Cited by 100 · see citing works

The Multiple RNA-Binding Domains of the mRNA Poly(A)-Binding Protein Have Different RNA-Binding Activities

Burd, C. G., Matunis, E. L., & Dreyfuss, G. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.7.3419-3424.1991 · Cited by 99 · see citing works

Computational identification of binding energy hot spots in protein–RNA complexes using an ensemble approach

Pan, Y., Wang, Z., Zhan, W., & Deng, L. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx822 · Cited by 92 · see citing works

Structure and Function of the Pre-mRNA Splicing Machine

Sperling, J. M., Azubel, M., & Sperling, R. (2008) · Structure · doi:10.1016/j.str.2008.08.011 · Cited by 88 · see citing works

Identification of RNA-binding Proteins in Macrophages by Interactome Capture

Liepelt, A., Vries, I. S. N., Simons, N., Eichelbaum, K., Föehr, S., Archer, S. K., Castelló, A., Usadel, B., Krijgsveld, J., Preiß, T., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.056564 · Cited by 86 · see citing works

RNA and protein 3D structure modeling: similarities and differences

Rother, K. M., Rother, M. B., Boniecki, M., Puton, T., & Bujnicki, J. M. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-010-0951-x · Cited by 85 · see citing works

RNA Structure Determination by NMR

Scott, L. G., & Hennig, M. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-159-2_2 · Cited by 82 · see citing works

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

Chen, Y. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh785 · Cited by 78 · see citing works

Sampling and scoring: A marriage made in heaven

Vajda, S., Hall, D. R., & Kozakov, D. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24343 · Cited by 77 · see citing works

RBind: computational network method to predict RNA binding sites

Wang, K., Jian, Y., Wang, H., Zeng, C., & Zhao, Y. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty345 · Cited by 77 · see citing works

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Huang, Y., Liu, S., Guo, D., Li, L., & Xiao, Y. (2013) · Scientific Reports · doi:10.1038/srep01887 · Cited by 70 · see citing works

YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

Purta, E., Kaminska, K. H., Kasprzak, J. M., Bujnicki, J. M., & Douthwaite, S. R. (2008) · RNA · doi:10.1261/rna.1198108 · Cited by 70 · see citing works

Efficient Restraints for Protein–Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment

Chelliah, V., Blundell, T. L., & Fernández‐Recio, J. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.01.001 · Cited by 69 · see citing works

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

Miao, Z., & Westhof, É. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004639 · Cited by 68 · see citing works

How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes?

Šponer, J., Krepl, M., Banáš, P., Kührová, P., Zgarbová, M., Jurečka, P., Havrila, M., & Otyepka, M. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1405 · Cited by 67 · see citing works

Identification of near‐native structures by clustering protein docking conformations

Lorenzen, S., & Zhang, Y. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21442 · Cited by 65 · see citing works

A coarse-grained force field for Protein–RNA docking

Setny, P., & Zacharias, M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr636 · Cited by 63 · see citing works

STRUCTURAL PREDICTION OF PROTEIN-RNA INTERACTION BY COMPUTATIONAL DOCKING WITH PROPENSITY-BASED STATISTICAL POTENTIALS

Pérez‐Cano, L., Solernou, A., Pons, C., & Fernández‐Recio, J. (2009) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814295291_0031 · Cited by 62 · see citing works

An account of solvent accessibility in protein-RNA recognition

Mukherjee, S., & Bahadur, R. P. (2018) · Scientific Reports · doi:10.1038/s41598-018-28373-2 · Cited by 60 · see citing works

A nonredundant structure dataset for benchmarking protein‐RNA computational docking

Huang, S., & Zou, X. (2012) · Journal of Computational Chemistry · doi:10.1002/jcc.23149 · Cited by 57 · see citing works

Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

Miao, Z., & Westhof, É. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv446 · Cited by 55 · see citing works

Molecular architecture of protein-RNA recognition sites

Barik, A., Nithin, C., Pilla, S. P., & Bahadur, R. P. (2015) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1004652 · Cited by 52 · see citing works

A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data

Pérez‐Cano, L., Jiménez‐García, B., & Fernández‐Recio, J. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24075 · Cited by 51 · see citing works

Computational modeling of RNA 3D structures and interactions

Dawson, W., & Bujnicki, J. M. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.11.007 · Cited by 50 · see citing works

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions

Maravić-Vlahoviček, G. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg666 · Cited by 48 · see citing works

A knowledge‐based potential function predicts the specificity and relative binding energy of RNA‐binding proteins

Zheng, S., Robertson, T. A., & Varani, G. (2007) · FEBS Journal · doi:10.1111/j.1742-4658.2007.06155.x · Cited by 47 · see citing works

A non-redundant protein-RNA docking benchmark version 2.0

Nithin, C., Mukherjee, S., & Bahadur, R. P. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25211 · Cited by 47 · see citing works

Probing binding hot spots at protein–RNA recognition sites

Barik, A., Nithin, C., Karampudi, N. B. R., Mukherjee, S., & Bahadur, R. P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv876 · Cited by 46 · see citing works

A new residue‐nucleotide propensity potential with structural information considered for discriminating protein‐RNA docking decoys

Li, C. H., Cao, L. B., Su, J. G., Yang, Y. X., & Wang, C. X. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23117 · Cited by 46 · see citing works

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

Liu, L., Xiong, Y., Gao, H., Wei, D., Mitchell, J. C., & Zhu, X. (2018) · Database · doi:10.1093/database/bay034 · Cited by 46 · see citing works

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods

Patel, T. R., Chojnowski, G., Astha, A., Koul, A., McKenna, S. A., & Bujnicki, J. M. (2016) · Methods · doi:10.1016/j.ymeth.2016.12.002 · Cited by 45 · see citing works

A protein–RNA docking benchmark (I): Nonredundant cases

Barik, A., Nithin, C., Manasa, P., & Bahadur, R. P. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24083 · Cited by 43 · see citing works

Template-Based Modeling of Protein-RNA Interactions

Zheng, J., Kundrotas, P. J., Vakser, I. A., & Liu, S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005120 · Cited by 42 · see citing works

Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue

Laer, B. V., Roovers, M., Wauters, L., Kasprzak, J. M., Dyzma, M., Deyaert, E., Singh, R. K., Feller, A., Bujnicki, J. M., Droogmans, L., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1369 · Cited by 39 · see citing works

From Structure to Function of RNA Binding Domains

Lorkovic, Z. (2012) · CRC Press eBooks · doi:10.1201/9781498713368-15 · Cited by 38 · see citing works

Structured non-coding RNAs and the RNP Renaissance

Hogg, J. R., & Collins, K. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.09.027 · Cited by 38 · see citing works

Hydration of protein–RNA recognition sites

Barik, A., & Bahadur, R. P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku679 · Cited by 37 · see citing works

M3: an integrative framework for structure determination of molecular machines

Karaca, E., Rodrigues, J., Graziadei, A., Bonvin, A. M. J. J., & Carlomagno, T. (2017) · Nature Methods · doi:10.1038/nmeth.4392 · Cited by 37 · see citing works

Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities

Guilhot-Gaudeffroy, A., Froidevaux, C., Azé, J., & Bernauer, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108928 · Cited by 36 · see citing works

The dataset for protein–RNA binding affinity

Yang, X., Li, H., Huang, Y., & Liu, S. (2013) · Protein Science · doi:10.1002/pro.2383 · Cited by 36 · see citing works

Drosophila TDP-43 RNA-Binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers and Polycomb Response Elements

Swain, A., Misulovin, Z., Pherson, M., Gause, M., Mihindukulasuriya, K. A., Rickels, R. A., Shilatifard, A., & Dorsett, D. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006331 · Cited by 33 · see citing works

Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit

Husain, N., Obranić, S., Kościński, Ł., Seetharaman, J., Babić, F., Bujnicki, J. M., Maravić-Vlahoviček, G., & Sivaraman, J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1033 · Cited by 32 · see citing works

Improved Accuracy in RNA–Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function

Iwakiri, J., Hamada, M., Asai, K., & Kameda, T. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b00254 · Cited by 31 · see citing works

Sequence-specific cleavage of dsRNA by Mini-III RNase

Głów, D., Pianka, D., Sulej, A., Kozlowski, L. P., Czarnecka, J., Chojnowski, G., Skowronek, K. J., & Bujnicki, J. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv009 · Cited by 28 · see citing works

Multiscale modeling of macromolecular biosystems

Flores, S. C., Bernauer, J., Shin, S., Zhou, R., & Huang, X. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbr077 · Cited by 28 · see citing works

Detailed close-ups and the big picture of spliceosomes

Jurica, M. S. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.05.005 · Cited by 24 · see citing works

Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome

Zhao, H., Yang, Y., Janga, S. C., Kao, C. C., & Zhou, Y. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24441 · Cited by 24 · see citing works

Protein-RNA Docking Using ICM

Arnautova, Y. A., Abagyan, R. A., & Totrov, M. M. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b00293 · Cited by 24 · see citing works

PRince: a web server for structural and physicochemical analysis of Protein-RNA interface

Barik, A., Mishra, A., & Bahadur, R. P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks535 · Cited by 23 · see citing works

Genome-wide survey of putative RNA-binding proteins encoded in the human proteome

Ghosh, P., & Sowdhamini, R. (2015) · Molecular BioSystems · doi:10.1039/c5mb00638d · Cited by 21 · see citing works

Structural Insight into Inhibition of CsrA-RNA Interaction Revealed by Docking, Molecular Dynamics and Free Energy Calculations

Ren, X., Zeng, R., Tortorella, M. D., Wang, J., & Wang, C. (2017) · Scientific Reports · doi:10.1038/s41598-017-14916-6 · Cited by 21 · see citing works

Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2′ 5′-oligoadenylate synthetase family

Deo, S. R., Patel, T. R., Chojnowski, G., Koul, A., Dzananovic, E., McEleney, K., Bujnicki, J. M., & McKenna, S. A. (2015) · Journal of Structural Biology · doi:10.1016/j.jsb.2015.04.005 · Cited by 20 · see citing works

FILTREST3D: discrimination of structural models using restraints from experimental data

Gajda, M. J., Tuszyńska, I., Kaczor-Kamińska, M., Bakulina, A., & Bujnicki, J. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq582 · Cited by 20 · see citing works

Structural and energy determinants in protein-RNA docking

Pérez‐Cano, L., Romero‐Durana, M., & Fernández‐Recio, J. (2016) · Methods · doi:10.1016/j.ymeth.2016.11.001 · Cited by 20 · see citing works

Defining distance restraints in HADDOCK

Bonvin, A. M. J. J., Karaca, E., Kastritis, P. L., & Rodrigues, J. (2018) · Nature Protocols · doi:10.1038/s41596-018-0017-6 · Cited by 20 · see citing works

PEPSI-Dock: a detailed data-driven protein–protein interaction potential accelerated by polar Fourier correlation

Neveu, É., Ritchie, D. W., Popov, P. A., & Grudinin, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw443 · Cited by 19 · see citing works

Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

Yan, Z., & Wang, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074443 · Cited by 18 · see citing works

Using 3dRPC for RNA–protein complex structure prediction

Huang, Y., Li, H., & Xiao, Y. (2016) · Biophysics Reports · doi:10.1007/s41048-017-0034-y · Cited by 17 · see citing works

Analysis of base-pairing probabilities of RNA molecules involved in protein–RNA interactions

Iwakiri, J., Kameda, T., Asai, K., & Hamada, M. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt453 · Cited by 13 · see citing works

Meta-server for automatic analysis, scoring and ranking of docking models

Anashkina, A. A., Kravatsky, Y. V., Kuznetsov, E., Makarov, A. А., & Adzhubei, A. A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx591 · Cited by 12 · see citing works

Modeling of Protein–RNA Complex Structures Using Computational Docking Methods

Madan, B., Kasprzak, J. M., Tuszyńska, I., Magnus, M., Szczepaniak, K., Dawson, W., & Bujnicki, J. M. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3569-7_21 · Cited by 10 · see citing works

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Ghosh, P., Mathew, O. K., & Sowdhamini, R. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1289-x · Cited by 8 · see citing works

hRBPome: a central repository of all known human RNA-binding proteinsPreprint

Ghosh, P., Murugavel, P., & Sowdhamini, R. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/269043 · Cited by 8 · see citing works

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

Bastard, K., Saladin, A., & Prévost, C. (2011) · International Journal of Molecular Sciences · doi:10.3390/ijms12021316 · Cited by 7 · see citing works

Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases

Głów, D., Kurkowska, M., Czarnecka, J., Szczepaniak, K., Pianka, D., Kappert, V., Bujnicki, J. M., & Skowronek, K. J. (2016) · Scientific Reports · doi:10.1038/srep38612 · Cited by 6 · see citing works

A Graph Approach to Mining Biological Patterns in the Binding Interfaces

Cheng, W., & Yan, C. (2016) · Journal of Computational Biology · doi:10.1089/cmb.2016.0128 · Cited by 5 · see citing works

RNA Worlds: From Life's Origins to Diversity in Gene Regulation. Edited by John F. Atkins, Raymond F. Gesteland, and Thomas R. Cech. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. $158.00. xvii + 361 p.; ill.; index. ISBN: 978-0-87969-946-8. 2011.

Koonin, E. V. (2012) · The Quarterly Review of Biology · doi:10.1086/663891 · Cited by 3 · see citing works

The HDOCK server for integrated protein–protein docking

Yan, Y., Tao, H., He, J., & Huang, S. (2020) · Nature Protocols · doi:10.1038/s41596-020-0312-x · Cited by 1,867 · see citing works

Protein–RNA interaction prediction with deep learning: structure matters

Wei, J., Chen, S., Zong, L., Gao, X., & Li, Y. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab540 · Cited by 92 · see citing works

Integrative Modelling of Biomolecular Complexes

Koukos, P. I., & Bonvin, A. M. J. J. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.11.009 · Cited by 89 · see citing works

A review of the current trends in computational approaches in drug design and metabolism

Ouma, R. B. O., Ngari, S. M., & Kibet, J. K. (2024) · Discover Public Health · doi:10.1186/s12982-024-00229-3 · Cited by 69 · see citing works

NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes

Feng, Y., Zhang, K., Wu, Q., & Huang, S. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00341 · Cited by 68 · see citing works

Challenges in protein docking

Vakser, I. A. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.07.001 · Cited by 62 · see citing works

Evaluating native-like structures of RNA-protein complexes through the deep learning method

Zeng, C., Jian, Y., Vosoughi, S., Zeng, C., & Zhao, Y. (2023) · Nature Communications · doi:10.1038/s41467-023-36720-9 · Cited by 54 · see citing works

ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid–Ligand Interactions

Feng, Y., & Huang, S. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00974 · Cited by 49 · see citing works

P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking

Zheng, J., Hong, X., Xie, J., Tong, X., & Liu, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz478 · Cited by 31 · see citing works

Coarse-grained (hybrid) integrative modeling of biomolecular interactions

Roel‐Touris, J., & Bonvin, A. M. J. J. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.05.002 · Cited by 31 · see citing works

Investigating RNA–protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations

Pavan, M., Bassani, D., Sturlese, M., & Moro, S. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac088 · Cited by 30 · see citing works

Protein-ensemble–RNA docking by efficient consideration of protein flexibility through homology models

He, J., Tao, H., & Huang, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz388 · Cited by 24 · see citing works

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

Wang, K., Hu, G., Wu, Z., Su, H. L., Yang, J., & Kurgan, L. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21186879 · Cited by 24 · see citing works

Multitasking Na+/Taurocholate Cotransporting Polypeptide (NTCP) as a Drug Target for HBV Infection: From Protein Engineering to Drug Discovery

Zakrzewicz, D., & Geyer, J. (2022) · Biomedicines · doi:10.3390/biomedicines10010196 · Cited by 23 · see citing works

Computational tools to study RNA-protein complexes

Bheemireddy, S., Sandhya, S., Srinivasan, N., & Sowdhamini, R. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.954926 · Cited by 23 · see citing works

RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity

Koralewska, N., Szczepańska, A., Ciechanowska, K., Wojnicka, M., Pokornowska, M., Milewski, M. C., Gudanis, D., Baranowski, D., Nithin, C., Bujnicki, J. M., et al. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03795-w · Cited by 20 · see citing works

A structure-based model for the prediction of protein–RNA binding affinity

Nithin, C., Mukherjee, S., & Bahadur, R. P. (2019) · RNA · doi:10.1261/rna.071779.119 · Cited by 19 · see citing works

Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins

Sarnowski, C. P., Bikaki, M., & Leitner, A. (2022) · Structure · doi:10.1016/j.str.2022.03.003 · Cited by 17 · see citing works

Computational approaches to macromolecular interactions in the cell

Vakser, I. A., & Deeds, E. J. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.03.012 · Cited by 15 · see citing works

Repurposing antiviral drugs against HTLV-1 protease by molecular docking and molecular dynamics simulation

Jahantigh, H. R., Ahmadi, N., Lovreglio, P., Stufano, A., Enayatkhani, M., Shahbazi, B., & Ahmadi, K. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2078411 · Cited by 14 · see citing works

Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction

Zeng, C., Chen, Z., Gao, J., Liu, H., & Zhao, Y. (2024) · Biomolecules · doi:10.3390/biom14101245 · Cited by 11 · see citing works

Systems biology in inflammatory bowel diseases: on the way to precision medicine

Dovrolis, N. (2019) · Annals of Gastroenterology · doi:10.20524/aog.2019.0373 · Cited by 11 · see citing works

A comparative study of the efficiency of HCV NS3/4A protease drugs against different HCV genotypes using in silico approaches

Ezat, A. A., & Elshemey, W. M. (2018) · Life Sciences · doi:10.1016/j.lfs.2018.12.004 · Cited by 9 · see citing works

RNA-protein interaction prediction without high-throughput data: An overview and benchmark of in silico tools

Krautwurst, S., & Lamkiewicz, K. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.11.015 · Cited by 7 · see citing works

Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools

Coskuner‐Weber, O., & Uversky, V. N. (2024) · Current Protein and Peptide Science · doi:10.2174/0113892037314062240618193044 · Cited by 7 · see citing works

Post-Docking Refinement of Peptide or Protein-RNA Complexes Using Thermal Titration Molecular Dynamics (TTMD): A Stability Insight

Dodaro, A., Novello, G., Menin, S., Strascia, C. C., Sturlese, M., Salmaso, V., & Moro, S. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01393 · Cited by 7 · see citing works

MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands

González‐Alemán, R., Chevrollier, N., Simoes, M., Montero, L. A., & Leclerc, F. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c01339 · Cited by 7 · see citing works

Bioinformatics evaluation of anticancer properties of GP63 protein-derived peptides on MMP2 protein of melanoma cancer

Sharifi, F., Sharifi, I., Babaei, Z., Alahdin, S., & Afgar, A. (2023) · Journal of Pathology Informatics · doi:10.1016/j.jpi.2023.100190 · Cited by 7 · see citing works

Methods and applications of RNA contact prediction*

Wang, H., & Zhao, Y. (2020) · Chinese Physics B · doi:10.1088/1674-1056/abb7f3 · Cited by 6 · see citing works

Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity

Kant, S., Nithin, C., Mukherjee, S., Maity, A., & Bahadur, R. P. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26825 · Cited by 5 · see citing works

Databases and web-based tools for studying structures of protein-nucleic acid complexes.

Dapkūnas, J., & Venclovas, Č. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103079 · 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

Special Issue: Computational Analysis of RNA Structure and Function

Gorodkin, J. (2019) · Genes · doi:10.3390/genes10010055 · Cited by 4 · see citing works

Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches

Barhoon, M., & Mahdiuni, H. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01029 · Cited by 3 · see citing works

An Overview of Bioinformatics and its Application: A Ray of Hope towards Microbial Biotechnology

Ghosh, R., Bera, R. D., & -, S. C. C. (2024) · International Journal For Multidisciplinary Research · doi:10.36948/ijfmr.2024.v06i01.13726 · Cited by 3 · see citing works

Computational Modeling Methods for 3D Structure Prediction of Ribozymes

Ghosh, P., Nithin, C., Joshi, A., Stefaniak, F., Wirecki, T. K., & Bujnicki, J. M. (2021) · doi:10.1002/9783527814527.ch33 · Cited by 3 · see citing works

Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts

Mahmoudi, I., Quignot, C., Martins, C., & Andreani, J. (2024) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012650 · Cited by 4 · see citing works

Molecular Docking and Computational In Silico Investigations of Metal-Based Drug Agents

Arjmand, F., Tabassum, S., & Khan, H. Y. (2024) · Springer eBooks · doi:10.1007/978-981-97-0146-9_6 · Cited by 2 · see citing works

Highlights from the ‘Noncoding RNA world: From Mechanism to Therapy’ conference, July 21-23, 2021

Saadeldin, M. K. (2021) · World Academy of Sciences Journal · doi:10.3892/wasj.2021.135 · Cited by 2 · see citing works

Statistical potentials for RNA-protein interactions optimized by CMA-ES

Kimura, T. D., Yasuo, N., Sekijima, M., & Lustig, B. (2021) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2021.108044 · Cited by 1 · see citing works

Computational modeling of intrinsically disordered and phase-separated protein states

Coskuner‐Weber, O., & Uversky, V. N. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21809-5.00015-6 · Cited by 1 · see citing works

Principles of computational drug designing and drug repurposing—An algorithmic approach

Bagchi, A. (2023) · Elsevier eBooks · doi:10.1016/b978-0-443-15280-1.00011-x · Cited by 1 · see citing works

Analysing microbial proteins: bioinformatic approaches for molecular structure and function characterization

Sarkar, S., Yadav, M., & Kumar, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-31550-3.00002-0 · Cited by 1 · see citing works

MCSS-based Docking and Improved Scoring of Protein-Nucleotide Complexes: I. A step forward to the Fragment-Based Design of OligonucleotidesPreprint

Chevrollier, N., & Leclerc, F. (2019) · HAL Portal Artxiker (Hindustan Aeronautics Limited (India)) · doi:10.1101/622068

STRAND: Structure Refinement of RNA-Protein Complexes via DiffusionPreprint

Al-zeqri, M., Franke, J. K. H., & Runge, F. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.30.662415

Overcoming translational barriers in RNA–protein docking: enhancing computational accuracy for targeted drug discovery

Akram, H., Rahman, M. U., Mazhar, S., Qamer, F., & Yousaf, A. (2025) · Future Medicinal Chemistry · doi:10.1080/17568919.2025.2533061

Evaluation of protein–RNA Docking Web Servers for Template-Free Docking and Comparison with the AlphaFold Server

Chong, N. H. H., Tan, E. Z. T., Tan, C. H. E., Ilangovan, H., Lim, Y. J., Srivastava, A., & Tan, Y. S. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01990

Fragment-based modelling of protein-RNA complexes for protein design

Kravchenko, A. (2023) · theses.fr (ABES) · doi:10.70675/e211ffb4z6d6fz476ez9441z34c4cdf8d79a

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Huang, Y., Liu, S., Guo, D., Li, L., & Xiao, Y. (2013) · Scientific Reports · doi:10.1038/srep01887 · Cited by 70 · see citing works

3dRPC: a web server for 3D RNA–protein structure prediction

Huang, Y., Li, H., & Xiao, Y. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx742 · Cited by 32 · see citing works

Using 3dRPC for RNA–protein complex structure prediction

Huang, Y., Li, H., & Xiao, Y. (2016) · Biophysics Reports · doi:10.1007/s41048-017-0034-y · Cited by 17 · see citing works

Computational modeling of protein–RNA complex structures

Tuszyńska, I., Matelska, D., Magnus, M., Chojnowski, G., Kasprzak, J. M., Kozlowski, L. P., Dunin-Horkawicz, S., & Bujnicki, J. M. (2013) · Methods · doi:10.1016/j.ymeth.2013.09.014 · Cited by 33 · see citing works

Modeling of Protein–RNA Complex Structures Using Computational Docking Methods

Madan, B., Kasprzak, J. M., Tuszyńska, I., Magnus, M., Szczepaniak, K., Dawson, W., & Bujnicki, J. M. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3569-7_21 · Cited by 10 · see citing works