| Year |
Citation |
Score |
| 2024 |
Reys V, Giulini M, Cojocaru V, Engel A, Xu X, Roel-Touris J, Geng C, Ambrosetti F, Jiménez-García B, Jandova Z, Koukos PI, van Noort C, Teixeira JMC, van Keulen SC, Réau M, et al. Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55. Proteins. PMID 39739354 DOI: 10.1002/prot.26789 |
0.819 |
|
| 2024 |
Honorato RV, Trellet ME, Jiménez-García B, Schaarschmidt JJ, Giulini M, Reys V, Koukos PI, Rodrigues JPGLM, Karaca E, van Zundert GCP, Roel-Touris J, van Noort CW, Jandová Z, Melquiond ASJ, Bonvin AMJJ. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nature Protocols. PMID 38886530 DOI: 10.1038/s41596-024-01011-0 |
0.779 |
|
| 2023 |
van der Krift F, Zijlmans DW, Shukla R, Javed A, Koukos PI, Schwarz LL, Timmermans-Sprang EP, Maas PE, Gahtory D, van den Nieuwboer M, Mol JA, Strous GJ, Bonvin AM, van der Stelt M, Veldhuizen EJ, et al. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. Life Science Alliance. 6. PMID 37591722 DOI: 10.26508/lsa.202302058 |
0.451 |
|
| 2021 |
Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, ... ... Koukos PI, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. PMID 34453465 DOI: 10.1002/prot.26222 |
0.764 |
|
| 2021 |
Koukos PI, Réau M, Bonvin AMJJ. Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. Journal of Chemical Information and Modeling. PMID 34436890 DOI: 10.1021/acs.jcim.1c00796 |
0.815 |
|
| 2021 |
Honorato RV, Koukos PI, Jiménez-García B, Tsaregorodtsev A, Verlato M, Giachetti A, Rosato A, Bonvin AMJJ. Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. Frontiers in Molecular Biosciences. 8: 729513. PMID 34395534 DOI: 10.3389/fmolb.2021.729513 |
0.695 |
|
| 2021 |
Matos-Filipe P, Preto AJ, Koukos PI, Mourão J, Bonvin AMJJ, Moreira IS. MENSAdb: a thorough structural analysis of membrane protein dimers. Database : the Journal of Biological Databases and Curation. 2021. PMID 33822911 DOI: 10.1093/database/baab013 |
0.642 |
|
| 2019 |
Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue LC, Honorato RV, Moreira I, Kurkcuoglu Z, Vangone A, Bonvin AMJJ. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins. PMID 31886559 DOI: 10.1002/Prot.25869 |
0.69 |
|
| 2019 |
Basciu A, Koukos PI, Malloci G, Bonvin AMJJ, Vargiu AV. Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 31720895 DOI: 10.1007/s10822-019-00244-6 |
0.672 |
|
| 2019 |
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Koukos PI, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838 |
0.753 |
|
| 2019 |
Jiménez-García B, Elez K, Koukos PI, Bonvin AMJJ, Vangone A. PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. Bioinformatics (Oxford, England). PMID 31141126 DOI: 10.1093/bioinformatics/btz437 |
0.713 |
|
| 2019 |
Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet ME, Xue LC, Bonvin AMJJ. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics (Oxford, England). 35: 1585-1587. PMID 31051038 DOI: 10.1093/bioinformatics/bty816 |
0.772 |
|
| 2019 |
Preto AJ, Matos-Filipe P, Koukos PI, Renault P, Sousa SF, Moreira IS. Structural Characterization of Membrane Protein Dimers. Methods in Molecular Biology (Clifton, N.J.). 1958: 403-436. PMID 30945231 DOI: 10.1007/978-1-4939-9161-7_21 |
0.604 |
|
| 2018 |
Koukos PI, Faro I, van Noort CW, Bonvin AMJJ. A Membrane Protein Complex Docking Benchmark. Journal of Molecular Biology. PMID 30414967 DOI: 10.1016/j.jmb.2018.11.005 |
0.327 |
|
| 2018 |
Koukos PI, Xue LC, Bonvin AMJJ. Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. Journal of Computer-Aided Molecular Design. PMID 30128928 DOI: 10.1007/s10822-018-0148-4 |
0.432 |
|
| 2017 |
Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. Journal of Computer-Aided Molecular Design. PMID 28831657 DOI: 10.1007/S10822-017-0049-Y |
0.728 |
|
| 2017 |
Moreira IS, Koukos PI, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gümüş ZH, Costa J, Bonvin AMJJ. SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Scientific Reports. 7: 8007. PMID 28808256 DOI: 10.1038/S41598-017-08321-2 |
0.776 |
|
| 2017 |
Almeida JG, Preto AJ, Koukos PI, Bonvin AMJJ, Moreira IS. MEMBRANE PROTEINS STRUCTURES: A review on computational modeling tools. Biochimica Et Biophysica Acta. PMID 28716627 DOI: 10.1016/j.bbamem.2017.07.008 |
0.606 |
|
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