Low-resolution structural modeling of protein interactome
Open accessAbstract
Structural characterization of protein-protein interactions across the broad spectrum of scales is key to our understanding of life at the molecular level. Low-resolution approach to protein interactions is needed for modeling large interaction networks, given the significant level of uncertainties in large biomolecular systems and the high-throughput nature of the task. Since only a fraction of protein structures in interactome are determined experimentally, protein docking approaches are increasingly focusing on modeled proteins. Current rapid advancement of template-based modeling of protein-protein complexes is following a long standing trend in structure prediction of individual proteins. Protein-protein templates are already available for almost all interactions of structurally characterized proteins, and about one third of such templates are likely correct.
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?
Protein shape, reflecting the protein fold, to a large extent determines the docking solution, even at coarse-grained representation.
“Another important consideration is that the protein shape, reflecting the protein fold, to a large extent determines the docking solution, even at coarse-grained representation [11].”
From Challenges in protein docking (2020) · cites this paper as [11]
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
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
Gray, J. J., Moughon, S. E., Wang, C., Schueler‐Furman, O., Kuhlman, B. A., Rohl, C. A., & Baker, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00670-3 · Cited by 1,130 · see citing works
Csermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.04.009 · Cited by 821 · see citing works
Structure-based prediction of protein–protein interactions on a genome-wide scale
Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature · doi:10.1038/nature11503 · Cited by 723 · see citing works
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
McGuffee, S. R., & Elcock, A. H. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000694 · Cited by 693 · see citing works
Global dynamics of proteins: bridging between structure and function
Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.093008.131258 · Cited by 610 · see citing works
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
Ando, T., & Skolnick, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011354107 · Cited by 412 · see citing works
Structure-Based Assembly of Protein Complexes in Yeast
Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.-C., Bork, P., Superti-Furga, G., Serrano, L., et al. (2004) · Science · doi:10.1126/science.1092645 · Cited by 383 · see citing works
Nature of the protein universe
Levitt, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905029106 · Cited by 316 · see citing works
Physical limits of cells and proteomes
Dill, K. A., Ghosh, K., & Schmit, J. D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114477108 · Cited by 298 · see citing works
Lu, L. J., Lu, H. J., & Skolnick, J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10222 · Cited by 240 · see citing works
A systematic study of low-resolution recognition in protein-protein complexes
Vakser, I. A., Matar, O. G., & Lam, C. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.15.8477 · Cited by 180 · see citing works
Self-citationTemplates 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
Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination
Mukherjee, S., & Zhang, Y. (2011) · Structure · doi:10.1016/j.str.2011.04.006 · Cited by 174 · see citing works
Sircar, A., & Gray, J. J. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000644 · Cited by 166 · see citing works
Protein interface conservation across structure space
Zhang, Q. C., Petrey, D., Norel, R., & Honig, B. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005894107 · Cited by 156 · see citing works
Gao, M., & Skolnick, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012820107 · Cited by 139 · see citing works
Feig, M., & Sugita, Y. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp209302e · Cited by 139 · see citing works
Effects of Macromolecular Crowding on Protein Conformational Changes
Dong, H., Qin, S., & Zhou, H. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000833 · Cited by 110 · see citing works
Predicting the accuracy of protein–ligand docking on homology models
Bordogna, A., Pandini, A., & Bonati, L. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21601 · Cited by 107 · see citing works
Tovchigrechko, A., Wells, C. A., & Vakser, I. A. (2002) · Protein Science · doi:10.1110/ps.4730102 · Cited by 103 · see citing works
Toward a quantitative theory of intrinsically disordered proteins and their function
Liu, J., Faeder, J. R., & Camacho, C. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907710106 · Cited by 102 · see citing works
How common is the funnel‐like energy landscape in protein‐protein interactions?
Tovchigrechko, A., & Vakser, I. A. (2001) · Protein Science · doi:10.1110/ps.8701 · Cited by 100 · see citing works
iAlign: a method for the structural comparison of protein–protein interfaces
Gao, M., & Skolnick, J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq404 · Cited by 98 · see citing works
Three-dimensional modeling of protein interactions and complexes is going ‘omics
Stein, A., Mosca, R., & Aloy, P. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.005 · Cited by 94 · see citing works
Coarse-graining of multiprotein assemblies
Saunders, M. G., & Voth, G. A. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.01.003 · Cited by 93 · see citing works
Predicting protein-protein interface residues using local surface structural similarity
Jordan, R. A., EL‐Manzalawy, Y., Dobbs, D. L., & Honavar, V. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-41 · Cited by 92 · see citing works
Challenges for the prediction of macromolecular interactions
Wass, M. N., David, A., & Sternberg, M. J. E. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.013 · Cited by 88 · see citing works
Docking by structural similarity at protein‐protein interfaces
Sinha, R., Kundrotas, P. J., & Vakser, I. A. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22812 · Cited by 85 · see citing works
Capillarity theory for the fly-casting mechanism
Trizac, E., Levy, Y., & Wolynes, P. G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914727107 · Cited by 82 · 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
Blind predictions of protein interfaces by docking calculations in CAPRI
Lensink, M. F., & Wodak, S. J. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22850 · Cited by 80 · see citing works
D OCKGROUND system of databases for protein recognition studies: Unbound structures for docking
Gao, Y. D., Douguet, D., Tovchigrechko, A., & Vakser, I. A. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21714 · Cited by 76 · see citing works
Prediction of protein–protein binding free energies
Vreven, T., Hwang, H., Pierce, B. G., & Weng, Z. (2012) · Protein Science · doi:10.1002/pro.2027 · Cited by 76 · see citing works
Protein docking prediction using predicted protein-protein interface
Li, B., & Kihara, D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-7 · Cited by 75 · see citing works
Karaca, E., & Bonvin, A. M. J. J. (2011) · Structure · doi:10.1016/j.str.2011.01.014 · Cited by 71 · see citing works
Mosca, R., Pons, C., Fernández‐Recio, J., & Aloy, P. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000490 · Cited by 70 · see citing works
Vácha, R., & Frenkel, D. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.07.046 · Cited by 68 · see citing works
Ensemble Docking from Homology Models
Novoa, E. M., de Pouplana, L. R., Barril, X., & Orozco, M. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100246y · Cited by 67 · see citing works
Lasker, K., Šali, A., & Wolfson, H. J. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22845 · Cited by 67 · see citing works
Constructing structural networks of signaling pathways on the proteome scale
Kuzu, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.04.004 · Cited by 64 · see citing works
Li, X., Moal, I. H., & Bates, P. A. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22770 · Cited by 61 · see citing works
Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective
Ravikumar, K. M., Huang, W., & Yang, S. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.07.013 · Cited by 56 · see citing works
Human Proteome-scale Structural Modeling of E2–E3 Interactions Exploiting Interface Motifs
Kar, G., Keskin, Ö., Nussinov, R., & Gürsoy, A. (2011) · Journal of Proteome Research · doi:10.1021/pr2009143 · Cited by 54 · see citing works
Docking without docking: ISEARCH—prediction of interactions using known interfaces
Günther, S., May, P., Hoppe, A., Frömmel, C., & Preißner, R. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21746 · Cited by 53 · see citing works
Liu, S., & Vakser, I. A. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-280 · Cited by 52 · see citing works
Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data
Zhang, Z., & Voth, G. A. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100374a · Cited by 51 · see citing works
GWIDD: Genome-wide protein docking database
Kundrotas, P. J., Zhu, Z., & Vakser, I. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp944 · Cited by 47 · see citing works
Tunçbağ, N., Keskin, Ö., Nussinov, R., & Gürsoy, A. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24022 · Cited by 46 · see citing works
Main-chain complementarity in protein-protein recognition
Vakser, I. A. (1996) · Protein Engineering Design and Selection · doi:10.1093/protein/9.9.741 · Cited by 46 · see citing works
Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling
Kundrotas, P. J., & Vakser, I. A. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000727 · Cited by 45 · see citing works
Computational Protein-Protein Interactions
Nussinov, R., & Schreiber, G. (2009) · CRC Press eBooks · doi:10.1201/9781420070071 · Cited by 43 · see citing works
Shape complementarity of protein–protein complexes at multiple resolutions
Zhang, Q., Sanner, M. F., & Olson, A. J. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22256 · Cited by 37 · see citing works
Spatial clustering of protein binding sites for template based protein docking
Ghoorah, A. W., Devignes, M., Smaïl‐Tabbone, M., & Ritchie, D. W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr493 · Cited by 37 · see citing works
Sequence composition and environment effects on residue fluctuations in protein structures
Ruvinsky, A. M., & Vakser, I. A. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3498743 · Cited by 35 · see citing works
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach
Zen, A., Micheletti, C., Keskin, Ö., & Nussinov, R. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-26 · Cited by 33 · see citing works
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes
Abyzov, A. S., Bjornson, R. D., Felipe, M. A., & Gerstein, M. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22544 · Cited by 33 · see citing works
A simple shape characteristic of protein–protein recognition
Nicola, G., & Vakser, I. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm018 · Cited by 33 · see citing works
Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?
Sinha, R., Kundrotas, P. J., & Vakser, I. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031349 · Cited by 32 · see citing works
Side-Chain Conformational Changes upon Protein–Protein Association
Ruvinsky, A. M., Kirys, T., Tuzikov, A. V., & Vakser, I. A. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.02.030 · Cited by 32 · see citing works
A simple shape characteristic of protein–protein recognition
Nicola, G., & Vakser, I. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm303 · Cited by 31 · see citing works
Docking by Structural Similarity at Protein-Protein Interfaces
Kundrotas, P. J., Sinha, R., & Vakser, I. A. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.12.1043 · Cited by 29 · see citing works
Minimal ensembles of side chain conformers for modeling protein–protein interactions
Beglov, D., Hall, D. R., Brenke, R., Shapovalov, M. V., Dunbrack, R. L., Kozakov, D., & Vajda, S. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23222 · Cited by 27 · see citing works
Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling
Bryliński, M., & Skolnick, J. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21395 · Cited by 25 · see citing works
Burton, B. N., Zimmermann, M. T., Jernigan, R. L., & Wang, Y. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002530 · Cited by 25 · see citing works
Kirys, T., Ruvinsky, A. M., Tuzikov, A. V., & Vakser, I. A. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24103 · Cited by 25 · see citing works
Vorobjev, Y. N. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21394 · Cited by 19 · see citing works
Konc, J., Depolli, M., Trobec, R., Rozman, K., & Janežič, D. (2012) · Journal of Computational Chemistry · doi:10.1002/jcc.23048 · Cited by 16 · see citing works
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions
Kundrotas, P. J., Zhu, Z., & Vakser, I. A. (2012) · Human Genomics · doi:10.1186/1479-7364-6-7 · Cited by 14 · see citing works
Fast protein binding site comparisons using visual words representation
Pang, B., Zhao, N., Korkin, D., & Shyu, C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts138 · Cited by 13 · see citing works
Accuracy of functional surfaces on comparatively modeled protein structures
Zhao, J., Dundas, J., Kachalo, S., Ouyang, Z., & Liang, J. (2011) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-011-9109-z · Cited by 12 · see citing works
Assessing the reconstruction of macromolecular assemblies with toleranced models
Dreyfus, T., Doye, V., & Cazals, F. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24092 · Cited by 10 · see citing works
Teyra, J., Hawkins, J., Zhu, H., & Pisabarro, M. T. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22897 · Cited by 9 · see citing works
SCPC: a method to structurally compare protein complexes
Koike, R., & Ota, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr654 · Cited by 9 · see citing works
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins
Kirys, T., Ruvinsky, A. M., Tuzikov, A. V., & Vakser, I. A. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-236 · Cited by 8 · see citing works
LARGE-SCALE STRUCTURAL MODELING OF PROTEIN COMPLEXES AT LOW RESOLUTION
Zhu, Z., Tovchigrechko, A., BARONOVA, T., Gao, Y. D., Douguet, D., O’Toole, N., & Vakser, I. A. (2008) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720008003679 · Cited by 5 · see citing works
Vakser, I. A. (2009) · CRC Press eBooks · doi:10.1201/9781420070071.ch2 · Cited by 3 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
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
Self-citationModelling three-dimensional protein structures for applications in drug design
Schmidt, T., Bergner, A., & Schwede, T. F. (2013) · Drug Discovery Today · doi:10.1016/j.drudis.2013.10.027 · Cited by 187 · see citing works
Template-based structure modeling of protein–protein interactions
Szilágyi, A., & Zhang, Y. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.11.005 · Cited by 168 · see citing works
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
Huang, S. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.02.005 · Cited by 164 · see citing works
Interactome INSIDER: a structural interactome browser for genomic studies
Meyer, M. J., Beltrán, J. F., Liang, S., Fragoza, R., Rumack, A., Liang, J. H., Wei, X., & Yu, H. (2018) · Nature Methods · doi:10.1038/nmeth.4540 · Cited by 162 · see citing works
Progress and challenges in predicting protein interfaces
Esmaielbeiki, R., Krawczyk, K., Knapp, B., Nebel, J., & Deane, C. M. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv027 · Cited by 130 · see citing works
Protein Modeling: What Happened to the “Protein Structure Gap”?
Schwede, T. F. (2013) · Structure · doi:10.1016/j.str.2013.08.007 · Cited by 125 · see citing works
Infection-derived lipids elicit an immune deficiency circuit in arthropods
Shaw, D. K., Wang, X., Brown, L. J., Chávez, A. S. O., Reif, K. E., Smith, A. A., Scott, A. J., McClure, E. E., Boradia, V. M., Hammond, H., et al. (2017) · Nature Communications · doi:10.1038/ncomms14401 · Cited by 116 · see citing works
Protein–protein interaction networks: the puzzling riches
Wodak, S. J., Vlasblom, J., Turinsky, A. L., & Pu, S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.08.002 · Cited by 109 · see citing works
Towards a detailed atlas of protein–protein interactions
Mosca, R., Pons, T., Ceol, A. G. M., Valencia, A., & Aloy, P. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.07.005 · Cited by 91 · see citing works
Andréani, J., Faure, G., & Guérois, R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt260 · Cited by 88 · see citing works
Dockground: A comprehensive data resource for modeling of protein complexes
Kundrotas, P. J., Anishchenko, I. V., Dauzhenka, T. A., Kotthoff, I., Mnevets, D., Copeland, M. M., & Vakser, I. A. (2017) · Protein Science · doi:10.1002/pro.3295 · Cited by 82 · see citing works
Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale
Cafarelli, T. M., Desbuleux, A., Wang, Y., Choi, S. G., Ridder, D. D., & Vidal, M. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.05.003 · Cited by 72 · see citing works
Challenges in structural approaches to cell modeling
Im, W., Liang, J., Olson, A. J., Zhou, H., Vajda, S., & Vakser, I. A. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.05.024 · Cited by 66 · see citing works
Evolution of protein interactions: From interactomes to interfaces
Andréani, J., & Guérois, R. (2014) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2014.05.010 · Cited by 64 · 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
Self-citationFluorescence-Based Protein Stability Monitoring—A Review
Gooran, N., & Kopra, K. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031764 · Cited by 62 · see citing works
Pathogens Use Structural Mimicry of Native Host Ligands as a Mechanism for Host Receptor Engagement
Drayman, N., Glick, Y., Ben-nun-Shaul, O., Zer, H., Zlotnick, A., Gerber, D., Schueler‐Furman, O., & Oppenheim, A. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.05.005 · Cited by 57 · see citing works
Template-based prediction of protein function
Petrey, D. S., Chen, T. S., Deng, L., Garzón, J. I., Hwang, H., Lasso, G., Lee, H., Silkov, A., & Honig, B. H. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.01.007 · Cited by 47 · see citing works
Park, H., Lee, H., & Seok, C. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.08.001 · Cited by 44 · 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
DaReUS-Loop: a web server to model multiple loops in homology models
Karami, Y., Rey, J., Postic, G., Murail, S., Tufféry, P., & de Vries, S. J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz403 · Cited by 38 · see citing works
Application of docking methodologies to modeled proteins
Singh, A., Dauzhenka, T. A., Kundrotas, P. J., Sternberg, M. J. E., & Vakser, I. A. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25889 · Cited by 41 · see citing works
Kundrotas, P. J., & Vakser, I. A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24392 · Cited by 37 · see citing works
Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites
Goncearenco, A., Shaytan, A. К., Shoemaker, B. A., & Panchenko, A. R. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.06.056 · Cited by 38 · see citing works
Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model
Anishchenko, I., Kundrotas, P. J., & Vakser, I. A. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2018.07.035 · Cited by 29 · see citing works
KBDOCK 2013: a spatial classification of 3D protein domain family interactions
Ghoorah, A. W., Devignes, M., Smaïl‐Tabbone, M., & Ritchie, D. W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1199 · Cited by 28 · see citing works
Modeling complexes of modeled proteins
Anishchenko, I. V., Kundrotas, P. J., & Vakser, I. A. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25183 · Cited by 26 · see citing works
Structural templates for comparative protein docking
Anishchenko, I. V., Kundrotas, P. J., Tuzikov, A. V., & Vakser, I. A. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24736 · Cited by 26 · see citing works
Protein-Protein Docking with Dynamic Residue Protonation States
Kilambi, K. P., Reddy, K., & Gray, J. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004018 · Cited by 24 · see citing works
He, J., Tao, H., & Huang, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz388 · Cited by 24 · see citing works
Dockground resource for protein recognition studies
Collins, K. W., Copeland, M. M., Kotthoff, I., Singh, A., Kundrotas, P. J., & Vakser, I. A. (2022) · Protein Science · doi:10.1002/pro.4481 · Cited by 22 · see citing works
Protein models: The Grand Challenge of protein docking
Anishchenko, I. V., Kundrotas, P. J., Tuzikov, A. V., & Vakser, I. A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24385 · Cited by 23 · see citing works
Protein models docking benchmark 2
Anishchenko, I. V., Kundrotas, P. J., Tuzikov, A. V., & Vakser, I. A. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24784 · Cited by 22 · see citing works
Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides
Mansbach, R. A., & Ferguson, A. L. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b05781 · Cited by 20 · see citing works
Kilambi, K. P., Pacella, M. S., Xu, J., Labonte, J. W., Porter, J. R., Muthu, P., Drew, K., Kuroda, D., Schueler‐Furman, O., Bonneau, R., et al. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24425 · Cited by 20 · see citing works
Scoring docking conformations using predicted protein interfaces
Esmaielbeiki, R., & Nebel, J. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-171 · Cited by 19 · see citing works
Rigid-Docking Approaches to Explore Protein–Protein Interaction Space
Matsuzaki, Y., Uchikoga, N., Ohue, M., & Akiyama, Y. (2016) · Advances in biochemical engineering, biotechnology · doi:10.1007/10_2016_41 · Cited by 17 · see citing works
ProPairs: A Data Set for Protein–Protein Docking
Krull, F., Korff, G., Elghobashi‐Meinhardt, N., & Knapp, E. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00082 · Cited by 16 · see citing works
Randhawa, V., & Pathania, S. (2020) · Briefings in Functional Genomics · doi:10.1093/bfgp/elaa015 · Cited by 15 · see citing works
Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes
Gemović, B., Šumonja, N., Davidović, R. S., Perović, V., & Veljković, N. (2018) · Current Medicinal Chemistry · doi:10.2174/0929867325666180214113704 · Cited by 15 · 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
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts
Soltanikazemi, E., Quadir, F., Roy, R. S., Guo, Z., & Cheng, J. (2022) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26269 · Cited by 15 · see citing works
Protein–protein alternative binding modes do not overlap
Kundrotas, P. J., & Vakser, I. A. (2013) · Protein Science · doi:10.1002/pro.2295 · Cited by 13 · see citing works
Simulated unbound structures for benchmarking of protein docking in the Dockground resource
Kirys, T., Ruvinsky, A. M., Singla, D., Tuzikov, A. V., Kundrotas, P. J., & Vakser, I. A. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0672-3 · Cited by 13 · see citing works
Shimoda, T., Ishida, T., Suzuki, S., Ohue, M., & Akiyama, Y. (2013) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/2506583.2506693 · Cited by 8 · see citing works
Cazals, F., Dreyfus, T., Sachdeva, S., & Shah, N. (2014) · Computer Graphics Forum · doi:10.1111/cgf.12270 · Cited by 7 · see citing works
Dockground scoring benchmarks for protein docking
Kotthoff, I., Kundrotas, P. J., & Vakser, I. A. (2022) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26306 · Cited by 6 · see citing works
Malladi, S. B., Powell, H. R., David, A., Islam, S. A., Copeland, M. M., Kundrotas, P. J., Sternberg, M. J. E., & Vakser, I. A. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167608 · Cited by 6 · see citing works
Li, J., Vervoorts, J., Carloni, P., Rossetti, G., & Lüscher, B. (2017) · BMC Bioinformatics · doi:10.1186/s12859-016-1411-0 · Cited by 6 · see citing works
Structural quality of unrefined models in protein docking
Anishchenko, I. V., Kundrotas, P. J., & Vakser, I. A. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25188 · Cited by 4 · see citing works
Protein-DNA complex structure modeling based on structural template
Xie, J., Zheng, J., Hong, X., Tong, X., Liu, X., Song, Q., Liu, S., & Liu, S. (2021) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2021.09.018 · Cited by 3 · see citing works
Gene ontology improves template selection in comparative protein docking
Hadarovich, A., Anishchenko, I. V., Tuzikov, A. V., Kundrotas, P. J., & Vakser, I. A. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25645 · Cited by 2 · see citing works
Deep Learning Approach with Rotate-Shift Invariant Input to Predict Protein Homodimer Structure
Hadarovich, A., Kalinouski, A., & Tuzikov, A. V. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-57821-3_27 · Cited by 2 · see citing works
Genome-Wide Structural Modeling of Protein-Protein Interactions
Anishchenko, I. V., Badal, V. D., Dauzhenka, T. A., Das, M., Tuzikov, A. V., Kundrotas, P. J., & Vakser, I. A. (2016) · Lecture notes in computer science · doi:10.1007/978-3-319-38782-6_8 · Cited by 1 · see citing works
Qazi, I. H., Yuan, T., Yang, S., Angel, C., & Liu, J. (2024) · Frontiers in Veterinary Science · doi:10.3389/fvets.2024.1429169 · Cited by 1 · see citing works
Prediction of Protein Function from Theoretical Models
Rigden, D. J., Cymerman, I. A., & Bujnicki, J. M. (2017) · Springer eBooks · doi:10.1007/978-94-024-1069-3_15 · Cited by 1 · see citing works
Cankara, F., Tunçbağ, N., Gürsoy, A., & Keskin, Ö. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.03.587755 · Cited by 1 · see citing works
Protein-Protein Interaction Network Prediction Based on Tertiary Structure Data
大上, 雅., & Ohue, M. (2014)
Development of protein-protein docking methodology and benchmarking environment
Anishchenko, I. V. (2016) · KU ScholarWorks (University of Kansas)
- Authors
- Vakser, I. A.
- Affiliations
- University of Kansas (US)
- Corresponding author
- Vakser, Ilya A
- ORCID
- Vakser, Ilya A
- Venue
- Current Opinion in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2013-04
- Volume
- 23
- Issue
- 2
- Pages
- 198-205
- ISSN
- 0959-440X (ISSN-L)
- PMC
- PMC3676717
- OpenAlex
- W2021343666
- Cited by
- 62
- References
- 77
- Citations by year
- 2024: 3 · 2022: 4 · 2021: 2 · 2020: 4 · 2019: 3 · 2018: 6 · 2017: 5 · 2016: 7 · 2015: 7 · 2014: 8 · 2013: 13
- FWCI
- 1.10
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Current Opinion in Structural Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- KU ScholarWorks (University of Kansas) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM074255)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein interaction, protein-protein interaction network, protein docking, template-based modeling, protein-protein complex, interaction networks, structural uncertainty
- MeSH terms
- Models, Molecular, Protein Binding, Proteins, Proteome, Protein Interaction Mapping, Molecular Docking Simulation
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
