Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery. Proceedings of the AAAI Conference on Artificial Intelligence, (37)12:14356â14364, Association for the Advancement of Artificial Intelligence (AAAI), June 2023. [PUMA: imported topic_lifescience] URL
Modeling conformational states of proteins with AlphaFold. Current Opinion in Structural Biology, (81):102645, Elsevier BV, August 2023. [PUMA: imported topic_lifescience] URL
Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants. Cold Spring Harbor Laboratory, October 2023. [PUMA: imported topic_lifescience] URL
Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. In Joanna Slusky (Eds.), PLOS Computational Biology, (20)3:e1011939, Public Library of Science (PLoS), March 2024. [PUMA: imported topic_lifescience] URL
Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants. Cold Spring Harbor Laboratory, June 2024. [PUMA: imported topic_lifescience] URL
Template-free prediction of a new monotopic membrane protein fold and oligomeric assembly by Alphafold2. Cold Spring Harbor Laboratory, July 2022. [PUMA: imported topic_lifescience] URL
Sampling alternative conformational states of transporters and receptors with AlphaFold2. eLife, (11)eLife Sciences Publications, Ltd, March 2022. [PUMA: imported topic_lifescience] URL
A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins. Journal of Proteome Research, (20)8:4089â4100, American Chemical Society (ACS), July 2021. [PUMA: imported topic_lifescience] URL
Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. Journal of Computer-Aided Molecular Design, (30)3:209â217, Springer Science and Business Media LLC, December 2015. [PUMA: imported topic_lifescience] URL
Strandâloopâstrand motifs: Prediction of hairpins and diverging turns in proteins. Proteins: Structure, Function, and Bioinformatics, (54)2:282â288, Wiley, December 2003. [PUMA: imported topic_lifescience] URL
Towards Generalizable Predictions for the Effects of Mutations on G-Protein Coupled Receptor Expression. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL
Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors. Cold Spring Harbor Laboratory, April 2023. [PUMA: imported topic_lifescience] URL
Using Neural Networks for 13C NMR Chemical Shift PredictionâComparison with Traditional Methods. Journal of Magnetic Resonance, (157)2:242â252, Elsevier BV, August 2002. [PUMA: imported topic_lifescience] URL
3D Deep Learning for Biological Function Prediction from Physical Fields. 2020 International Conference on 3D Vision (3DV), 928â937, IEEE, November 2020. [PUMA: imported topic_lifescience] URL
Computational Methods in Drug Discovery. In Eric L. Barker (Eds.), Pharmacological Reviews, (66)1:334â395, American Society for Pharmacology & Experimental Therapeutics (ASPET), December 2013. [PUMA: imported topic_lifescience] URL
BCL::EMAS â Enantioselective Molecular Asymmetry Descriptor for 3D-QSAR. Molecules, (17)8:9971â9989, MDPI AG, August 2012. [PUMA: imported topic_lifescience] URL
Benchmarking Peptide Structure Prediction with AlphaFold2. Cold Spring Harbor Laboratory, February 2022. [PUMA: imported topic_lifescience] URL
Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL
Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery. Frontiers in Pharmacology, (13)Frontiers Media SA, February 2022. [PUMA: imported topic_lifescience] URL
A Novel Method for Guiding Protein-Ligand Docking with QSAR-Derived Pharmacophore Maps. Biophysical Journal, (100)3:394aâ395a, Elsevier BV, February 2011. [PUMA: imported topic_lifescience] URL
Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL
Benchmarking AlphaMissense pathogenicity predictions against cystic fibrosis variants. In Jeffrey L Brodsky (Eds.), PLOS ONE, (19)1:e0297560, Public Library of Science (PLoS), January 2024. [PUMA: imported topic_lifescience] URL
Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. In Dina Schneidman (Eds.), PLOS Computational Biology, (18)12:e1010230, Public Library of Science (PLoS), December 2022. [PUMA: imported topic_lifescience] URL
Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions. arXiv, 2020. [PUMA: imported topic_lifescience] URL
SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL
Quantitative StructureâActivity Relationship Modeling of Kinase Selectivity Profiles. Molecules, (22)9:1576, MDPI AG, September 2017. [PUMA: imported topic_lifescience] URL
Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks. Journal of Chemical Information and Computer Sciences, (41)6:1535â1546, American Chemical Society (ACS), October 2001. [PUMA: imported topic_lifescience] URL
An Active Learning Framework Improves Tumor Variant Interpretation. Cancer Research, (82)15:2704â2715, American Association for Cancer Research (AACR), June 2022. [PUMA: imported topic_lifescience] URL
Heterogeneity of the GFP fitness landscape and data-driven protein design. Cold Spring Harbor Laboratory, December 2021. [PUMA: imported topic_lifescience] URL
Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences, (100)21:12105â12110, Proceedings of the National Academy of Sciences, October 2003. [PUMA: imported topic_lifescience] URL
Ligand-based virtual screen for the discovery of novel M5 inhibitor chemotypes. Bioorganic & Medicinal Chemistry Letters, (26)18:4487â4491, Elsevier BV, September 2016. [PUMA: imported topic_lifescience] URL
Sampling the conformational landscapes of transporters and receptors with AlphaFold2. Cold Spring Harbor Laboratory, November 2021. [PUMA: imported topic_lifescience] URL
VUStruct: a compute pipeline for high throughput and personalized structural biology. Cold Spring Harbor Laboratory, August 2024. [PUMA: imported topic_lifescience] URL
Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists. ACS Chemical Neuroscience, (15)12:2396â2407, American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL
A unified hydrophobicity scale for multispan membrane proteins. Proteins: Structure, Function, and Bioinformatics, (76)1:13â29, Wiley, December 2008. [PUMA: imported topic_lifescience] URL
BCL::Mol2Dâa robust atom environment descriptor for QSAR modeling and lead optimization. Journal of Computer-Aided Molecular Design, (33)5:477â486, Springer Science and Business Media LLC, April 2019. [PUMA: imported topic_lifescience] URL
Neural Network Prediction of 13C NMR Chemical Shifts of Substituted Benzenes. Monatshefte für Chemie / Chemical Monthly, (130)9:1089â1095, Springer Science and Business Media LLC, September 1999. [PUMA: imported topic_lifescience] URL
Improving quantitative structureâactivity relationship models using Artificial Neural Networks trained with dropout. Journal of Computer-Aided Molecular Design, (30)2:177â189, Springer Science and Business Media LLC, February 2016. [PUMA: imported topic_lifescience] URL
3D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators. Bioorganic & Medicinal Chemistry Letters, (20)19:5922â5924, Elsevier BV, October 2010. [PUMA: imported topic_lifescience] URL
Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife, (11)eLife Sciences Publications, Ltd, May 2022. [PUMA: imported topic_lifescience] URL
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. Journal of Chemical Information and Modeling, (61)2:603â620, American Chemical Society (ACS), January 2021. [PUMA: imported topic_lifescience] URL
Application of machine learning approaches on quantitative structure activity relationships. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 255â262, IEEE, March 2009. [PUMA: imported topic_lifescience] URL
GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 314â320, IEEE, May 2012. [PUMA: imported topic_lifescience] URL
Bcl∷ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimerâs Disease. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 329â334, IEEE, May 2012. [PUMA: imported topic_lifescience] URL
Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis. American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL
Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks. Journal of Chemical Information and Computer Sciences, (40)5:1169â1176, American Chemical Society (ACS), August 2000. [PUMA: imported topic_lifescience] URL
Predicting the functional impact of KCNQ1 variants with artificial neural networks. In Joanna Slusky (Eds.), PLOS Computational Biology, (18)4:e1010038, Public Library of Science (PLoS), April 2022. [PUMA: imported topic_lifescience] URL
Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks. QSAR & Combinatorial Science, (22)7:722â728, Wiley, October 2003. [PUMA: imported topic_lifescience] URL
Divergent Pairwise Epistasis in the Context of Unstable Membrane Protein Variants. eLife Sciences Publications, Ltd, December 2023. [PUMA: imported topic_lifescience] URL
Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2. Biophysical Journal, (122)11:2041â2052, Elsevier BV, June 2023. [PUMA: imported topic_lifescience] URL