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1A unified hydrophobicity scale for multispan membrane proteins
J. Koehler, N. Woetzel, R. Staritzbichler, C. Sanders, and J. Meiler. Proteins: Structure, Function, and Bioinformatics, 76 (1): 13â29 (December 2008)
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1BCL::Mol2Dâa robust atom environment descriptor for QSAR modeling and lead optimization
O. Vu, J. Mendenhall, D. Altarawy, and J. Meiler. Journal of Computer-Aided Molecular Design, 33 (5): 477â486 (April 2019)
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1Neural Network Prediction of 13C NMR Chemical Shifts of Substituted Benzenes
J. Meiler, R. Meusinger, and M. Will. Monatshefte fÃ¼r Chemie / Chemical Monthly, 130 (9): 1089â1095 (September 1999)
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1Improving quantitative structureâactivity relationship models using Artificial Neural Networks trained with dropout
J. Mendenhall, and J. Meiler. Journal of Computer-Aided Molecular Design, 30 (2): 177â189 (February 2016)
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13D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators
E. Lowe, A. Ferrebee, A. Rodriguez, P. Conn, and J. Meiler. Bioorganic & Medicinal Chemistry Letters, 20 (19): 5922â5924 (October 2010)
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1Heterogeneity of the GFP fitness landscape and data-driven protein design
L. Gonzalez Somermeyer, A. Fleiss, A. Mishin, N. Bozhanova, A. Igolkina, J. Meiler, M. Alaball Pujol, E. Putintseva, K. Sarkisyan, and F. Kondrashov. eLife, (May 2022)
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1General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps
B. Brown, J. Mendenhall, A. Geanes, and J. Meiler. Journal of Chemical Information and Modeling, 61 (2): 603â620 (January 2021)
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1Application of machine learning approaches on quantitative structure activity relationships
M. Butkiewicz, R. Mueller, D. Selic, E. Dawson, and J. Meiler. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, (March 2009)
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1GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data
E. Lowe, M. Butkiewicz, N. Woetzel, and J. Meiler. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), (May 2012)
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1Bcl&#x2237;ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimerâs Disease
M. Butkiewicz, E. Lowe, and J. Meiler. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), (May 2012)
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1Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis
J. DeCorte, B. Brown, and J. Meiler. (June 2024)
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1Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks
J. Meiler, R. Meusinger, and M. Will. Journal of Chemical Information and Computer Sciences, 40 (5): 1169â1176 (August 2000)
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1Predicting the functional impact of KCNQ1 variants with artificial neural networks
S. Phul, G. Kuenze, C. Vanoye, C. Sanders, A. George, and J. Meiler. PLOS Computational Biology, 18 (4): e1010038 (April 2022)
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1Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks
A. Bleckmann, and J. Meiler. QSAR & Combinatorial Science, 22 (7): 722â728 (October 2003)
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1Divergent Pairwise Epistasis in the Context of Unstable Membrane Protein Variants
L. Chamness, C. Kuntz, A. McKee, W. Penn, C. Hemmerich, D. Rusch, H. Woods, Dyotima, J. Meiler, and J. Schlebach. (December 2023)
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1Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2
A. Gulsevin, B. Han, J. Porta, H. Mchaourab, J. Meiler, and A. Kenworthy. Biophysical Journal, 122 (11): 2041â2052 (June 2023)
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1Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database
M. Butkiewicz, E. Lowe, R. Mueller, J. Mendenhall, P. Teixeira, C. Weaver, and J. Meiler. Molecules, 18 (1): 735â756 (January 2013)
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1Novel methods of automated structure elucidation based on 13C NMR spectroscopy
J. Meiler, and M. KÃ¶ck. Magnetic Resonance in Chemistry, 42 (12): 1042â1045 (October 2004)
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1Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations
B. Brown, R. Stein, J. Meiler, and H. Mchaourab. Journal of Chemical Theory and Computation, 20 (3): 1434â1447 (January 2024)
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1Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties
D. Sala, P. Hildebrand, and J. Meiler. Frontiers in Molecular Biosciences, (February 2023)
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1Approximating conformational Boltzmann distributions with AlphaFold2 predictions
B. Brown, R. Stein, J. Meiler, and H. Mchaourab. (August 2023)
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1Improved prediction of trans-membrane spans in proteins using an artificial neural network
J. Koehler, R. Mueller, and J. Meiler. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, (March 2009)
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1Comparative analysis of machine learning techniques for the prediction of logP
E. Lowe, M. Butkiewicz, M. Spellings, A. Omlor, and J. Meiler. 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), (April 2011)
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1Discovery of 2â(2âBenzoxazoyl amino)â4âArylâ5âCyanopyrimidine as Negative Allosteric Modulators (NAMs) of Metabotropic Glutamate Receptorâ5 (mGlu5): From an Artificial Neural Network Virtual Screen to an In Vivo Tool Compound
R. Mueller, E. Dawson, J. Meiler, A. Rodriguez, B. Chauder, B. Bates, A. Felts, J. Lamb, U. Menon, S. Jadhav and 9 other author(s). ChemMedChem, 7 (3): 406â414 (January 2012)
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1NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction
A. Al-Fatlawi, N. Afrin, C. Ozen, N. Malekian, and M. Schroeder. Frontiers in Bioinformatics, (March 2022)
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1Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances
S. Bolz, and M. Schroeder. Expert Opinion on Drug Discovery, 18 (9): 973–985 (July 2023)
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1A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance
N. Malekian, A. Agrawal, T. Berendonk, A. Al-Fatlawi, and M. Schroeder. Scientific Reports, (May 2022)
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1Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance
N. Malekian, S. Sainath, A. Al-Fatlawi, and M. Schroeder. Frontiers in Microbiology, (December 2023)
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1A community effort in SARS‐CoV‐2 drug discovery
J. Schimunek, P. Seidl, K. Elez, T. Hempel, T. Le, F. Noé, S. Olsson, L. Raich, R. Winter, H. Gokcan and 142 other author(s). Molecular Informatics, (November 2023)
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1An interaction-based drug discovery screen explains known SARS-CoV-2 inhibitors and predicts new compound scaffolds
P. Schake, K. Dishnica, F. Kaiser, C. Leberecht, V. Haupt, and M. Schroeder. Scientific Reports, (June 2023)
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1Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening
M. Adasme, S. Bolz, A. Al-Fatlawi, and M. Schroeder. Journal of Cheminformatics, (March 2022)
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1Targeting ion channels with ultra-large library screening for hit discovery
K. Melancon, P. Pliushcheuskaya, J. Meiler, and G. Künze. Frontiers in Molecular Neuroscience, (January 2024)
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1Ferric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency
R. Maniero, C. Picco, A. Hartmann, F. Engelberger, A. Gradogna, J. Scholz-Starke, M. Melzer, G. Künze, A. Carpaneto, N. von Wirén and 1 other author(s). Nature Communications, (January 2024)
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1Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain
P. Pliushcheuskaya, S. Kesh, E. Kaufmann, S. Wucherpfennig, F. Schwede, G. Künze, and V. Nache. ACS Chemical Neuroscience, 15 (8): 1652–1668 (April 2024)
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1Structural Studies on the Binding Mode of Bisphenols to PPARγ
A. Useini, I. Schwerin, G. Künze, and N. Sträter. Biomolecules, 14 (6): 640 (May 2024)
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1The First International Workshop on Open Web Search (WOWS)
S. Farzana, M. Fröbe, M. Granitzer, G. Hendriksen, D. Hiemstra, M. Potthast, and S. Zerhoudi. European Conference on Information Retrieval, page 426--431. Springer, (2024)
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1Impact and development of an Open Web Index for open web search
M. Granitzer, S. Voigt, N. Fathima, M. Golasowski, C. Guetl, T. Hecking, G. Hendriksen, D. Hiemstra, J. Martinovic, J. Mitrović and 1 other author(s). Journal of the Association for Information Science and Technology, 75 (5): 512--520 (2024)
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1Systematic Evaluation of Neural Retrieval Models on the Touché 2020 Argument Retrieval Subset of BEIR
N. Thakur, L. Bonifacio, M. Fröbe, A. Bondarenko, E. Kamalloo, M. Potthast, M. Hagen, and J. Lin. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, page 1420–1430. ACM, (July 2024)
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1Report on the Dagstuhl Seminar on Frontiers of Information Access Experimentation for Research and Education
C. Bauer, B. Carterette, N. Ferro, N. Fuhr, J. Beel, T. Breuer, C. Clarke, A. Crescenzi, G. Demartini, G. Di Nunzio and 1 other author(s). ACM SIGIR Forum, 57, page 1--28. ACM New York, NY, USA, (2023)
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1The Information Retrieval Experiment Platform (Extended Abstract)
M. Fröbe, J. Reimer, S. MacAvaney, N. Deckers, J. Bevendorff, B. Stein, M. Hagen, and M. Potthast. Lernen. Wissen. Daten. Analysen. -- LWDA 2023, page 179--191. CEUR-WS.org, (October 2023)
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1The Information Retrieval Experiment Platform (Extended Abstract)
M. Fröbe, J. Reimer, S. MacAvaney, N. Deckers, S. Reich, J. Bevendorff, B. Stein, M. Hagen, and M. Potthast. Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, page 8405–8410. International Joint Conferences on Artificial Intelligence Organization, (August 2024)
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1Prototyping Open Web Search Applications with TIRA: A Case Study in Research-oriented Teaching
M. Fröbe, T. Elstner, H. Scells, and M. Potthast. 5th International Symposium on Open Search Technology (OSSYM 2023), International Open Search Symposium, (October 2023)
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1Open Web Search at LongEval 2023: Reciprocal Rank Fusion on Automatically Generated Query Variants
M. Fröbe, G. Hendriksen, A. de Vries, and M. Potthast. (2023)
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1Overview of Touché 2024: Argumentation Systems
J. Kiesel, {. Cöltekin, M. Heinrich, M. Fröbe, M. Alshomary, B. De Longueville, T. Erjavec, N. Handke, M. Kopp, N. Ljubesić and 1 other author(s). (2024)
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1Overview of PAN 2024: Multi-author Writing Style Analysis, Multilingual Text Detoxification, Oppositional Thinking Analysis, and Generative AI Authorship Verification Condensed Lab Overview
A. Ayele, N. Babakov, J. Bevendorff, X. Casals, B. Chulvi, D. Dementieva, A. Elnagar, D. Freitag, M. Fröbe, D. Korencić and 1 other author(s). International Conference of the Cross-Language Evaluation Forum for European Languages, page 231--259. Springer, (2024)
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1Resources for Combining Teaching and Research in Information Retrieval Coursework
M. Fröbe, H. Scells, T. Elstner, C. Akiki, L. Gienapp, J. Reimer, S. MacAvaney, B. Stein, M. Hagen, and M. Potthast. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, page 1115–1125. ACM, (July 2024)
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1The infinite index: Information retrieval on generative text-to-image models
N. Deckers, M. Fröbe, J. Kiesel, G. Pandolfo, C. Schröder, B. Stein, and M. Potthast. Proceedings of the 2023 conference on human information interaction and retrieval, page 172--186. (2023)
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1Evaluating Generative Ad Hoc Information Retrieval
L. Gienapp, H. Scells, N. Deckers, J. Bevendorff, S. Wang, J. Kiesel, S. Syed, M. Fröbe, G. Zuccon, B. Stein and 2 other author(s). Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, page 1916–1929. ACM, (July 2024)
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1Trigger Warnings: Bootstrapping a Violence Detector for Fan Fiction
M. Wolska, M. Wiegmann, C. Schröder, O. Borchardt, B. Stein, and M. Potthast. Findings of the Association for Computational Linguistics: EMNLP 2023, page 569–576. Association for Computational Linguistics, (2023)
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1Small-Text: Active Learning for Text Classification in Python
C. Schröder, L. Müller, A. Niekler, and M. Potthast. Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations, page 84--95. Dubrovnik, Croatia, Association for Computational Linguistics, (May 2023)
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