TY - JOUR A1 - Donati, Luca A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Augmented ant colony algorithm for virtual drug discovery JF - Journal of Mathematical Chemistry N2 - Docking is a fundamental problem in computational biology and drug discovery that seeks to predict a ligand’s binding mode and affinity to a target protein. However, the large search space size and the complexity of the underlying physical interactions make docking a challenging task. Here, we review a docking method, based on the ant colony optimization algorithm, that ranks a set of candidate ligands by solving a minimization problem for each ligand individually. In addition, we propose an augmented version that takes into account all energy functions collectively, allowing only one minimization problem to be solved. The results show that our modification outperforms in accuracy and efficiency. Y1 - 2023 U6 - https://doi.org/10.1007/s10910-023-01549-6 VL - 62 SP - 367 EP - 385 ER - TY - JOUR A1 - Schimunek, Johannes A1 - Seidl, Philipp A1 - Elez, Katarina A1 - Hempel, Tim A1 - Le, Tuan A1 - Noé, Frank A1 - Olsson, Simon A1 - Raich, Lluís A1 - Winter, Robin A1 - Gokcan, Hatice A1 - Gusev, Filipp A1 - Gutkin, Evgeny M. A1 - Isayev, Olexandr A1 - Kurnikova, Maria G. A1 - Narangoda, Chamali H. A1 - Zubatyuk, Roman A1 - Bosko, Ivan P. A1 - Furs, Konstantin V. A1 - Karpenko, Anna D. A1 - Kornoushenko, Yury V. A1 - Shuldau, Mikita A1 - Yushkevich, Artsemi A1 - Benabderrahmane, Mohammed B. A1 - Bousquet-Melou, Patrick A1 - Bureau, Ronan A1 - Charton, Beatrice A1 - Cirou, Bertrand C. A1 - Gil, Gérard A1 - Allen, William J. A1 - Sirimulla, Suman A1 - Watowich, Stanley A1 - Antonopoulos, Nick A1 - Epitropakis, Nikolaos A1 - Krasoulis, Agamemnon A1 - Itsikalis, Vassilis A1 - Theodorakis, Stavros A1 - Kozlovskii, Igor A1 - Maliutin, Anton A1 - Medvedev, Alexander A1 - Popov, Petr A1 - Zaretckii, Mark A1 - Eghbal-Zadeh, Hamid A1 - Halmich, Christina A1 - Hochreiter, Sepp A1 - Mayr, Andreas A1 - Ruch, Peter A1 - Widrich, Michael A1 - Berenger, Francois A1 - Kumar, Ashutosh A1 - Yamanishi, Yoshihiro A1 - Zhang, Kam Y. J. A1 - Bengio, Emmanuel A1 - Bengio, Yoshua A1 - Jain, Moksh J. A1 - Korablyov, Maksym A1 - Liu, Cheng-Hao A1 - Marcou, Gilles A1 - Glaab, Enrico A1 - Barnsley, Kelly A1 - Iyengar, Suhasini M. A1 - Ondrechen, Mary Jo A1 - Haupt, V. Joachim A1 - Kaiser, Florian A1 - Schroeder, Michael A1 - Pugliese, Luisa A1 - Albani, Simone A1 - Athanasiou, Christina A1 - Beccari, Andrea A1 - Carloni, Paolo A1 - D’Arrigo, Giulia A1 - Gianquinto, Eleonora A1 - Goßen, Jonas A1 - Hanke, Anton A1 - Joseph, Benjamin P. A1 - Kokh, Daria B. A1 - Kovachka, Sandra A1 - Manelfi, Candida A1 - Mukherjee, Goutam A1 - Muñiz-Chicharro, Abraham A1 - Musiani, Francesco A1 - Nunes-Alves, Ariane A1 - Paiardi, Giulia A1 - Rossetti, Giulia A1 - Sadiq, S. Kashif A1 - Spyrakis, Francesca A1 - Talarico, Carmine A1 - Tsengenes, Alexandros A1 - Wade, Rebecca C. A1 - Copeland, Conner A1 - Gaiser, Jeremiah A1 - Olson, Daniel R. A1 - Roy, Amitava A1 - Venkatraman, Vishwesh A1 - Wheeler, Travis J. A1 - Arthanari, Haribabu A1 - Blaschitz, Klara A1 - Cespugli, Marco A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Fischer, Patrick D. A1 - Gorgulla, Christoph A1 - Gruber, Christian A1 - Gruber, Karl A1 - Hetmann, Michael A1 - Kinney, Jamie E. A1 - Padmanabha Das, Krishna M. A1 - Pandita, Shreya A1 - Singh, Amit A1 - Steinkellner, Georg A1 - Tesseyre, Guilhem A1 - Wagner, Gerhard A1 - Wang, Zi-Fu A1 - Yust, Ryan J. A1 - Druzhilovskiy, Dmitry S. A1 - Filimonov, Dmitry A. A1 - Pogodin, Pavel V. A1 - Poroikov, Vladimir A1 - Rudik, Anastassia V. A1 - Stolbov, Leonid A. A1 - Veselovsky, Alexander V. A1 - De Rosa, Maria A1 - De Simone, Giada A1 - Gulotta, Maria R. A1 - Lombino, Jessica A1 - Mekni, Nedra A1 - Perricone, Ugo A1 - Casini, Arturo A1 - Embree, Amanda A1 - Gordon, D. Benjamin A1 - Lei, David A1 - Pratt, Katelin A1 - Voigt, Christopher A. A1 - Chen, Kuang-Yu A1 - Jacob, Yves A1 - Krischuns, Tim A1 - Lafaye, Pierre A1 - Zettor, Agnès A1 - Rodríguez, M. Luis A1 - White, Kris M. A1 - Fearon, Daren A1 - Von Delft, Frank A1 - Walsh, Martin A. A1 - Horvath, Dragos A1 - Brooks III, Charles L. A1 - Falsafi, Babak A1 - Ford, Bryan A1 - García-Sastre, Adolfo A1 - Yup Lee, Sang A1 - Naffakh, Nadia A1 - Varnek, Alexandre A1 - Klambauer, Günter A1 - Hermans, Thomas M. T1 - A community effort in SARS-CoV-2 drug discovery JF - Molecular Informatics KW - COVID-19 KW - drug discovery KW - machine learning KW - SARS-CoV-2 Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1002/minf.202300262 VL - 43 IS - 1 SP - e202300262 ER -