Search Results - "Koukos, Panagiotis"

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem by Honorato, Rodrigo V., Koukos, Panagiotis I., Jiménez-García, Brian, Tsaregorodtsev, Andrei, Verlato, Marco, Giachetti, Andrea, Rosato, Antonio, Bonvin, Alexandre M. J. J.

“…Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three…”
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Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories by Koukos, Panagiotis I., Glykos, Nicholas M.

“…We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories…”
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PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes by Jiménez-García, Brian, Elez, Katarina, Koukos, Panagiotis I, Bonvin, Alexandre Mjj, Vangone, Anna

“…Abstract Summary Distinguishing biologically relevant interfaces from crystallographic ones in biological complexes is fundamental in order to associate…”
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Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing by Koukos, Panagiotis I, Réau, Manon, Bonvin, Alexandre M. J. J

“…Small-molecule docking remains one of the most valuable computational techniques for the structure prediction of protein–small-molecule complexes. It allows us…”
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Membrane proteins structures: A review on computational modeling tools by Almeida, Jose G., Preto, Antonio J., Koukos, Panagiotis I., Bonvin, Alexandre M.J.J., Moreira, Irina S.

“…Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic…”
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Pathogen-sugar interactions revealed by universal saturation transfer analysis by Buchanan, Charles J, Gaunt, Ben, Harrison, Peter J, Yang, Yun, Liu, Jiwei, Khan, Aziz, Giltrap, Andrew M, Le Bas, Audrey, Ward, Philip N, Gupta, Kapil, Dumoux, Maud, Tan, Tiong Kit, Schimaski, Lisa, Daga, Sergio, Picchiotti, Nicola, Baldassarri, Margherita, Benetti, Elisa, Fallerini, Chiara, Fava, Francesca, Giliberti, Annarita, Koukos, Panagiotis I, Davy, Matthew J, Lakshminarayanan, Abirami, Xue, Xiaochao, Papadakis, Georgios, Deimel, Lachlan P, Casablancas-Antràs, Virgínia, Claridge, Timothy D W, Bonvin, Alexandre M J J, Sattentau, Quentin J, Furini, Simone, Gori, Marco, Huo, Jiandong, Owens, Raymond J, Schaffitzel, Christiane, Berger, Imre, Renieri, Alessandra, Naismith, James H, Baldwin, Andrew J, Davis, Benjamin G

“…Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded…”
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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications by Koukos, Panagiotis I., Dehghani-Ghahnaviyeh, Sepehr, Velez-Vega, Camilo, Manchester, John, Tieleman, D. Peter, Duca, José S., Souza, Paulo C. T., Cournia, Zoe

“…Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to…”
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SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots by Moreira, Irina S., Koukos, Panagiotis I., Melo, Rita, Almeida, Jose G., Preto, Antonio J., Schaarschmidt, Joerg, Trellet, Mikael, Gümüş, Zeynep H., Costa, Joaquim, Bonvin, Alexandre M. J. J.

“…We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with…”
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A Membrane Protein Complex Docking Benchmark by Koukos, Panagiotis I., Faro, Inge, van Noort, Charlotte W., Bonvin, Alexandre M.J.J.

“…We report the first membrane protein–protein docking benchmark consisting of 37 targets of diverse functions and folds. The structures were chosen based on a…”
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Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4 by Basciu, Andrea, Koukos, Panagiotis I., Malloci, Giuliano, Bonvin, Alexandre M. J. J., Vargiu, Attilio V.

“…We report the performance of our newly introduced Ensemble Docking with Enhanced sampling of pocket Shape (EDES) protocol coupled to a template-based algorithm…”
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Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide by Koukos, Panagiotis I, Glykos, Nicholas M

“…Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences)…”
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Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 by Kurkcuoglu, Zeynep, Koukos, Panagiotis I., Citro, Nevia, Trellet, Mikael E., Rodrigues, J. P. G. L. M., Moreira, Irina S., Roel-Touris, Jorge, Melquiond, Adrien S. J., Geng, Cunliang, Schaarschmidt, Jörg, Xue, Li C., Vangone, Anna, Bonvin, A. M. J. J.

“…We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment,…”
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A click-flipped enzyme substrate boosts the performance of the diagnostic screening for Hunter syndrome by Schwarz, Markus, Skrinjar, Philipp, Fink, Michael J, Kronister, Stefan, Mechtler, Thomas, Koukos, Panagiotis I, Bonvin, Alexandre M. J. J, Kasper, David C, Mikula, Hannes

“…We report on the unexpected finding that click modification of iduronyl azides results in a conformational flip of the pyranose ring, which led to the…”
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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes by Honorato, Rodrigo V., Trellet, Mikael E., Jiménez-García, Brian, Schaarschmidt, Jörg J., Giulini, Marco, Reys, Victor, Koukos, Panagiotis I., Rodrigues, João P. G. L. M., Karaca, Ezgi, van Zundert, Gydo C. P., Roel-Touris, Jorge, van Noort, Charlotte W., Jandová, Zuzana, Melquiond, Adrien S. J., Bonvin, Alexandre M. J. J.

“…Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the…”
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On the Application of Good-Turing Statistics to Quantify Convergence of Biomolecular Simulations by Koukos, Panagiotis I, Glykos, Nicholas M

“…Quantifying convergence and sufficient sampling of macromolecular molecular dynamics simulations is more often than not a source of controversy (and of various…”
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An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45 by Koukos, Panagiotis I., Roel‐Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Schaarschmidt, Jörg, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li C., Honorato, Rodrigo V., Moreira, Irina, Kurkcuoglu, Zeynep, Vangone, Anna, Bonvin, Alexandre M. J. J.

“…Our information‐driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part,…”
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Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3 by Koukos, Panagiotis I., Xue, Li C., Bonvin, Alexandre M. J. J.

“…We report the performance of HADDOCK in the 2018 iteration of the Grand Challenge organised by the D3R consortium. Building on the findings of our…”
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MENSAdb: a thorough structural analysis of membrane protein dimers by Matos-Filipe, Pedro, Preto, António J, Koukos, Panagiotis I, Mourão, Joana, Bonvin, Alexandre M J J, Moreira, Irina S

“…Membrane proteins (MPs) are key players in a variety of different cellular processes and constitute the target of around 60% of all Food and Drug…”
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A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance by van der Krift, Felix, Zijlmans, Dick W, Shukla, Rhythm, Javed, Ali, Koukos, Panagiotis I, Schwarz, Laura LE, Timmermans-Sprang, Elpetra PM, Maas, Peter EM, Gahtory, Digvijay, van den Nieuwboer, Maurits, Mol, Jan A, Strous, Ger J, Bonvin, Alexandre MJJ, van der Stelt, Mario, Veldhuizen, Edwin JA, Weingarth, Markus, Vermeulen, Michiel, Klumperman, Judith, Maurice, Madelon M

“…Cancer cells make extensive use of the folate cycle to sustain increased anabolic metabolism. Multiple chemotherapeutic drugs interfere with the folate cycle,…”
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Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server by Vangone, Anna, Schaarschmidt, Joerg, Koukos, Panagiotis, Geng, Cunliang, Citro, Nevia, Trellet, Mikael E, Xue, Li C, Bonvin, Alexandre M J J

“…Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein-protein complexes. By using a…”
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