Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks von Mamun, Abu Amar M. Al, Lombardo, Mary-Jane, Shee, Chandan, Lisewski, Andreas M., Gonzalez, Caleb, Lin, Dongxu, Nehring, Ralf B., Saint-Ruf, Claude, Gibson, Janet L., Frisch, Ryan L., Lichtarge, Olivier, Hastings, P. J., Rosenberg, Susan M.

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A large-scale evaluation of computational protein function prediction von Clark, Wyatt T, Oron, Tal Ronnen, Schnoes, Alexandra M, Wittkop, Tobias, Sokolov, Artem, Graim, Kiley, Funk, Christopher, Verspoor, Karin, Ben-Hur, Asa, Pandey, Gaurav, Yunes, Jeffrey M, Talwalkar, Ameet S, Repo, Susanna, Souza, Michael L, Piovesan, Damiano, Casadio, Rita, Wang, Zheng, Cheng, Jianlin, Fang, Hai, Gough, Julian, Koskinen, Patrik, Törönen, Petri, Nokso-Koivisto, Jussi, Holm, Liisa, Cozzetto, Domenico, Buchan, Daniel W A, Bryson, Kevin, Jones, David T, Limaye, Bhakti, Inamdar, Harshal, Datta, Avik, Manjari, Sunitha K, Joshi, Rajendra, Chitale, Meghana, Kihara, Daisuke, Lisewski, Andreas M, Erdin, Serkan, Venner, Eric, Lichtarge, Olivier, Rentzsch, Robert, Yang, Haixuan, Romero, Alfonso E, Bhat, Prajwal, Paccanaro, Alberto, Hamp, Tobias, Kaßner, Rebecca, Seemayer, Stefan, Vicedo, Esmeralda, Schaefer, Christian, Achten, Dominik, Auer, Florian, Boehm, Ariane, Braun, Tatjana, Hecht, Maximilian, Heron, Mark, Hönigschmid, Peter, Hopf, Thomas A, Kaufmann, Stefanie, Kiening, Michael, Krompass, Denis, Landerer, Cedric, Mahlich, Yannick, Roos, Manfred, Björne, Jari, Salakoski, Tapio, Wong, Andrew, Shatkay, Hagit, Gatzmann, Fanny, Sommer, Ingolf, Wass, Mark N, Sternberg, Michael J E, Škunca, Nives, Supek, Fran, Bošnjak, Matko, Panov, Panče, Džeroski, Sašo, Šmuc, Tomislav, Kourmpetis, Yiannis A I, van Dijk, Aalt D J, Braak, Cajo J F ter, Zhou, Yuanpeng, Gong, Qingtian, Dong, Xinran, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Di Camillo, Barbara, Toppo, Stefano, Lan, Liang, Djuric, Nemanja, Guo, Yuhong, Vucetic, Slobodan, Bairoch, Amos, Linial, Michal, Babbitt, Patricia C, Brenner, Steven E, Orengo, Christine, Mooney, Sean D, Friedberg, Iddo

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Plasmodium spp. membrane glutathione S-transferases: detoxification units and drug targets von Lisewski, Andreas M

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The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs von Chen, Brian Y, Fofanov, Viacheslav Y, Bryant, Drew H, Dodson, Bradley D, Kristensen, David M, Lisewski, Andreas M, Kimmel, Marek, Lichtarge, Olivier, Kavraki, Lydia E

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Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction von Chen, Brian Y., Fofanov, Viacheslav Y., Bryant, Drew H., Dodson, Bradley D., Kristensen, David M., Lisewski, Andreas M., Kimmel, Marek, Lichtarge, Olivier, Kavraki, Lydia E.

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Prediction of enzyme function based on 3D templates of evolutionarily important amino acids von Kristensen, David M, Ward, R Matthew, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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Safety and efficacy of ganaxolone in patients with CDKL5 deficiency disorder: results from the double-blind phase of a randomised, placebo-controlled, phase 3 trial von Knight, Elia M Pestana, Amin, Sam, Bahi-Buisson, Nadia, Benke, Tim A, Cross, J Helen, Demarest, Scott T, Olson, Heather E, Specchio, Nicola, Fleming, Thomas R, Aimetti, Alex A, Gasior, Maciej, Devinsky, Orrin, Belousova, Elena, Belyaev, Oleg, Ben-Zeev, Bruria, Brunklaus, Andreas, Ciliberto, Michael A., Darra, Francesca, Davis, Ronald, De Giorgis, Valentina, Doronina, Olga, Fahey, Michael, Guerrini, Renzo, Heydemann, Peter, Khaletskaya, Olga, Lisewski, Pawel, Marsh, Eric D., Moosa, Ahsan N., Perry, Scott, Philip, Sunny, Rajaraman, Rajsekar R., Renfroe, Ben, Saneto, Russell P., Scheffer, Ingrid E., Sogawa, Yoshimi, Suter, Bernhardt, Sweney, Matthew T., Tarquinio, Daniel, Veggiotti, Pierangelo, Wallace, Geoff, Weisenberg, Judy, Wilfong, Angus, Wirrell, Elaine C., Zafar, Muhammad, Zolnowska, Marta

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Potential role of Plasmodium falciparum exported protein 1 in the chloroquine mode of action von Lisewski, Andreas Martin, Quiros, Joel Patrick, Mittal, Monica, Putluri, Nagireddy, Sreekumar, Arun, Haeggström, Jesper Z., Lichtarge, Olivier

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De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features von Ward, R Matthew, Erdin, Serkan, Tran, Tuan A, Kristensen, David M, Lisewski, Andreas Martin, Lichtarge, Olivier

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Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity von Kristensen, David M., Chen, Brian Y., Fofanov, Viacheslav Y., Ward, R. Matthew, Lisewski, Andreas Martin, Kimmel, Marek, Kavraki, Lydia E., Lichtarge, Olivier

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PPV for each of the 53 proteins in the training set (highest PPV in red squares, others in purple diamonds) and for the templates with randomly chosen residues (green triangles, hi... von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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Annotation performance of ETA (black dashed hollow diamond), BLAST (cyan dashed hollow circle), PSI-BLAST (orange dashed hollow square), the intersection of BLAST+ETA (blue solid c... von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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PPV of BLAST (cyan dashed hollow circle) and BLAST+ETA (blue solid circle) as the maximum e-value cutoff for BLAST varies (horizontal axis) von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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Overlap (purple spheres) of ET Rank template residues (red spheres) with SITE records (green spheres) provided by the PDB, in the context of the surface trace cluster (red sticks)... von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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(a) Stacked cumulative histogram of RMSDs of significant (p-value ≤ 1%) matches, including matches with the same function (red) and different function (blue) von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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Match PPV of ETA (black dashed hollow diamond), BLAST (cyan dashed hollow circle), PSI-BLAST (orange dashed hollow square), the intersection of BLAST+ETA (blue solid circle), and t... von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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Venn diagram showing the overlap with true (purple) and false (white) matches to a) the PDB set and b) the PSI set, found by ETA (blue), BLAST (yellow), and PSI-BLAST (orange von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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Illustration of the automated functional annotation pipeline von Kristensen, David M, R Matthew Ward, Lisewski, Andreas Martin, Erdin, Serkan, Chen, Brian Y, Fofanov, Viacheslav Y, Kimmel, Marek, Kavraki, Lydia E, Lichtarge, Olivier

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