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1Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery
Y. Liu, Y. Wang, O. Vu, R. Moretti, B. Bodenheimer, J. Meiler, and T. Derr. Proceedings of the AAAI Conference on Artificial Intelligence, 37 (12): 14356â14364 (June 2023)
18 hours ago by @scadsfct
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2Modeling conformational states of proteins with AlphaFold
D. Sala, F. Engelberger, H. Mchaourab, and J. Meiler. Current Opinion in Structural Biology, (August 2023)
18 hours ago by @scadsfct
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1Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants
E. McDonald, K. Oliver, J. Schlebach, J. Meiler, and L. Plate. (October 2023)
18 hours ago by @scadsfct
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1Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins
M. Ertelt, V. Mulligan, J. Maguire, S. Lyskov, R. Moretti, T. Schiffner, J. Meiler, and C. Schoeder. PLOS Computational Biology, 20 (3): e1011939 (March 2024)
18 hours ago by @scadsfct
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1Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants
M. Ertelt, R. Moretti, J. Meiler, and C. Schoeder. (June 2024)
18 hours ago by @scadsfct
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1Template-free prediction of a new monotopic membrane protein fold and oligomeric assembly by Alphafold2
A. Gulsevin, B. Han, J. Porta, H. Mchaourab, J. Meiler, and A. Kenworthy. (July 2022)
18 hours ago by @scadsfct
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1Sampling alternative conformational states of transporters and receptors with AlphaFold2
D. del Alamo, D. Sala, H. Mchaourab, and J. Meiler. eLife, (March 2022)
18 hours ago by @scadsfct
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2A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins
B. Li, J. Mendenhall, J. Capra, and J. Meiler. Journal of Proteome Research, 20 (8): 4089â4100 (July 2021)
18 hours ago by @scadsfct
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1Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign
G. Sliwoski, J. Mendenhall, and J. Meiler. Journal of Computer-Aided Molecular Design, 30 (3): 209â217 (December 2015)
18 hours ago by @scadsfct
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1Strandâloopâstrand motifs: Prediction of hairpins and diverging turns in proteins
M. Kuhn, J. Meiler, and D. Baker. Proteins: Structure, Function, and Bioinformatics, 54 (2): 282â288 (December 2003)
18 hours ago by @scadsfct
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1Towards Generalizable Predictions for the Effects of Mutations on G-Protein Coupled Receptor Expression
C. Kuntz, H. Woods, A. McKee, N. Zelt, J. Mendenhall, J. Meiler, and J. Schlebach. (December 2021)
18 hours ago by @scadsfct
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1Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors
Y. Liu, R. Moretti, Y. Wang, H. Dong, B. Yan, B. Bodenheimer, T. Derr, and J. Meiler. (April 2023)
18 hours ago by @scadsfct
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1Using Neural Networks for 13C NMR Chemical Shift PredictionâComparison with Traditional Methods
J. Meiler, W. Maier, M. Will, and R. Meusinger. Journal of Magnetic Resonance, 157 (2): 242â252 (August 2002)
18 hours ago by @scadsfct
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13D Deep Learning for Biological Function Prediction from Physical Fields
V. Golkov, M. Skwark, A. Mirchev, G. Dikov, A. Geanes, J. Mendenhall, J. Meiler, and D. Cremers. 2020 International Conference on 3D Vision (3DV), (November 2020)
18 hours ago by @scadsfct
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1Computational Methods in Drug Discovery
G. Sliwoski, S. Kothiwale, J. Meiler, and E. Lowe. Pharmacological Reviews, 66 (1): 334â395 (December 2013)
18 hours ago by @scadsfct
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1BCL::EMAS â Enantioselective Molecular Asymmetry Descriptor for 3D-QSAR
G. Sliwoski, E. Lowe, M. Butkiewicz, and J. Meiler. Molecules, 17 (8): 9971â9989 (August 2012)
18 hours ago by @scadsfct
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1Benchmarking Peptide Structure Prediction with AlphaFold2
A. Gulsevin, and J. Meiler. (February 2022)
18 hours ago by @scadsfct
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1Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201
S. Jiang, Z. Su, N. Bloodworth, Y. Liu, C. Martina, D. Harrison, and J. Meiler. (November 2024)
18 hours ago by @scadsfct
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1Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery
B. Brown, O. Vu, A. Geanes, S. Kothiwale, M. Butkiewicz, E. Lowe, R. Mueller, R. Pape, J. Mendenhall, and J. Meiler. Frontiers in Pharmacology, (February 2022)
18 hours ago by @scadsfct
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1A Novel Method for Guiding Protein-Ligand Docking with QSAR-Derived Pharmacophore Maps
S. DeLuca, and J. Meiler. Biophysical Journal, 100 (3): 394aâ395a (February 2011)
18 hours ago by @scadsfct
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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. (December 2021)
18 hours ago by @scadsfct
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1Benchmarking AlphaMissense pathogenicity predictions against cystic fibrosis variants
E. McDonald, K. Oliver, J. Schlebach, J. Meiler, and L. Plate. PLOS ONE, 19 (1): e0297560 (January 2024)
18 hours ago by @scadsfct
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2Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods
M. Fischer, J. Crowe, and J. Meiler. PLOS Computational Biology, 18 (12): e1010230 (December 2022)
18 hours ago by @scadsfct
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1Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions
V. Golkov, A. Becker, D. Plop, D. Čuturilo, N. Davoudi, J. Mendenhall, R. Moretti, J. Meiler, and D. Cremers. (2020)
18 hours ago by @scadsfct
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1SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI
X. Kuang, z. su, Y. Liu, X. Lin, J. Smith, T. Derr, Y. Wu, and J. Meiler. (November 2024)
18 hours ago by @scadsfct
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1Quantitative StructureâActivity Relationship Modeling of Kinase Selectivity Profiles
S. Kothiwale, C. Borza, A. Pozzi, and J. Meiler. Molecules, 22 (9): 1576 (September 2017)
18 hours ago by @scadsfct
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1Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks
J. Meiler, and M. Will. Journal of Chemical Information and Computer Sciences, 41 (6): 1535â1546 (October 2001)
18 hours ago by @scadsfct
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2An Active Learning Framework Improves Tumor Variant Interpretation
A. Blee, B. Li, T. Pecen, J. Meiler, Z. Nagel, J. Capra, and W. Chazin. Cancer Research, 82 (15): 2704â2715 (June 2022)
18 hours ago by @scadsfct
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1Heterogeneity of the GFP fitness landscape and data-driven protein design
L. Somermeyer, A. Fleiss, A. Mishin, N. Bozhanova, A. Igolkina, J. Meiler, M. Pujol, E. Putintseva, K. Sarkisyan, and F. Kondrashov. (December 2021)
18 hours ago by @scadsfct
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1Coupled prediction of protein secondary and tertiary structure
J. Meiler, and D. Baker. Proceedings of the National Academy of Sciences, 100 (21): 12105â12110 (October 2003)
18 hours ago by @scadsfct
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1Ligand-based virtual screen for the discovery of novel M5 inhibitor chemotypes
A. Geanes, H. Cho, K. Nance, K. McGowan, P. Conn, C. Jones, J. Meiler, and C. Lindsley. Bioorganic & Medicinal Chemistry Letters, 26 (18): 4487â4491 (September 2016)
18 hours ago by @scadsfct
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1Sampling the conformational landscapes of transporters and receptors with AlphaFold2
D. del Alamo, D. Sala, H. Mchaourab, and J. Meiler. (November 2021)
18 hours ago by @scadsfct
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1VUStruct: a compute pipeline for high throughput and personalized structural biology
C. Moth, J. Sheehan, A. Mamun, R. Sivley, A. Gulsevin, D. Rinker, J. Capra, and J. Meiler. (August 2024)
18 hours ago by @scadsfct
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1Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists
C. Jones, B. Brown, D. Schultz, J. Engers, V. Kramlinger, J. Meiler, and C. Lindsley. ACS Chemical Neuroscience, 15 (12): 2396â2407 (June 2024)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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2General 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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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)
18 hours ago by @scadsfct
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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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