Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks. - Jens Meiler; Reinhard Meusinger; Martin Will (J. Chem. Inf. Comput. Sci., 2000)

Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks. - Jens Meiler; Martin Will (J. Chem. Inf. Comput. Sci., 2001)

Validation of Structural Proposals by Substructure Analysis and 13C NMR Chemical Shift Prediction. - Jens Meiler; Erdogan Sanli; Jochen Junker; Reinhard Meusinger; Thomas Lindel; Martin Will; Walter Maier; Matthias Köck (J. Chem. Inf. Comput. Sci., 2002)

Small Molecules as Rotamers: Generation and Docking in RosettaLigand. - Kristian Kaufmann; Jens Meiler (German Conference on Bioinformatics, 2008)

Application of machine learning approaches on quantitative structure activity relationships. - Mariusz Butkiewicz; Ralf Mueller; Danilo Selic; Eric Dawson; Jens Meiler (CIBCB, 2009)

Improved prediction of trans-membrane spans in proteins using an artificial neural network. - Julia Koehler; Ralf Mueller; Jens Meiler (CIBCB, 2009)

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family. - Gregory D. Friedland; Nils-Alexander Lakomek; Christian Griesinger; Jens Meiler; Tanja Kortemme (PLoS Comput. Biol., 2009)

BCL: : Contact-Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and De Novo Structure Determination. - Mert Karakas; Nils Woetzel; Jens Meiler (J. Comput. Biol., 2010)

Comparative analysis of machine learning techniques for the prediction of logP. - Edward W. Lowe; Mariusz Butkiewicz; Matthew Spellings; Albert Omlor; Jens Meiler (CIBCB, 2011)

Bcl: : Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System. - Nathan Alexander; Nils Woetzel; Jens Meiler (ICCABS, 2011)

Poster: GPU-accelerated artificial neural network for QSAR modeling. - Edward W. Lowe; Nils Woetzel; Jens Meiler (ICCABS, 2011)

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps. - Edward W. Lowe; Nils Woetzel; Jens Meiler (ICCABS, 2011)

Bcl∷ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimer's Disease. - Mariusz Butkiewicz; Edward W. Lowe; Jens Meiler (CIBCB, 2012)

GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data. - Edward W. Lowe; Mariusz Butkiewicz; Nils Woetzel; Jens Meiler (CIBCB, 2012)

Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. - Steffen Lindert; Phoebe L. Stewart; Jens Meiler (Comput. Biol. Chem., 2013)

Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. - Joseph J. Crivelli; Gordon Lemmon; Kristian Kaufmann; Jens Meiler (J. Comput. Aided Mol. Des., 2013)

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies. - Jordan R. Willis; Bryan S. Briney; Samuel L. DeLuca; James E. Crowe Jr.; Jens Meiler (PLoS Comput. Biol., 2013)

BCL: : Conf: small molecule conformational sampling using a knowledge based rotamer library. - Sandeepkumar Kothiwale; Jeffrey L. Mendenhall; Jens Meiler (J. Cheminformatics, 2015)

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. - Alexander M. Sevy; Tim M. Jacobs; James E. Crowe Jr.; Jens Meiler (PLoS Comput. Biol., 2015)

Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images. - Vladimir Golkov; Marcin J. Skwark; Antonij Golkov; Alexey Dosovitskiy; Thomas Brox; Jens Meiler; Daniel Cremers (NIPS, 2016)

Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout. - Jeffrey L. Mendenhall; Jens Meiler (J. Comput. Aided Mol. Des., 2016)

Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. - Gregory Sliwoski; Jeffrey L. Mendenhall; Jens Meiler (J. Comput. Aided Mol. Des., 2016)

Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. - Bian Li; Jeffrey L. Mendenhall; Elizabeth Dong Nguyen; Brian E. Weiner; Axel W. Fischer; Jens Meiler (J. Chem. Inf. Model., 2016)

Consensus queries in ligand-based virtual screening experiments. - Francois Berenger; Oanh Vu; Jens Meiler (J. Cheminformatics, 2017)

Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. - R. Michael Sivley; Jonathan H. Sheehan; Jonathan A. Kropski; Joy D. Cogan; Timothy S. Blackwell; John A. Phillips; William S. Bush; Jens Meiler; John A. Capra (BMC Bioinform., 2018)

Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. - Steven A. Combs; Benjamin K. Mueller; Jens Meiler (J. Chem. Inf. Model., 2018)

Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. - Darwin Y. Fu; Jens Meiler (J. Chem. Inf. Model., 2018)

Integrating linear optimization with structural modeling to increase HIV neutralization breadth. - Alexander M. Sevy; Swetasudha Panda; James E. Crowe Jr.; Jens Meiler; Yevgeniy Vorobeychik (PLoS Comput. Biol., 2018)

Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures. - Alexander M. Sevy; Cinque S. Soto; Robin G. Bombardi; Jens Meiler; James E. Crowe Jr. (BMC Bioinform., 2019)

BCL: : Mol2D - a robust atom environment descriptor for QSAR modeling and lead optimization. - Oanh Vu; Jeffrey L. Mendenhall; Doaa Altarawy; Jens Meiler (J. Comput. Aided Mol. Des., 2019)

BCL: : MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping. - Benjamin P. Brown; Jeffrey L. Mendenhall; Jens Meiler (J. Chem. Inf. Model., 2019)

3D Deep Learning for Biological Function Prediction from Physical Fields. - Vladimir Golkov; Marcin J. Skwark; Atanas Mirchev; Georgi Dikov; Alexander R. Geanes; Jeffrey L. Mendenhall; Jens Meiler; Daniel Cremers (3DV, 2020)

Foldit Drug Design Game Usability Study: Comparison of Citizen and Expert Scientists. - Yunchao Liu 001; Rocco Moretti; Bobby Bodenheimer; Jens Meiler (MIG, 2020)

PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. - Cinque S. Soto; Jessica A. Finn; Jordan R. Willis; Samuel B. Day; Robert S. Sinkovits; Taylor Jones; Samuel Schmitz; Jens Meiler; Andre Branchizio; James E. Crowe Jr. (BMC Bioinform., 2020)

Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions. - Vladimir Golkov; Alexander Becker; Daniel T. Plop; Daniel Cuturilo; Neda Davoudi; Jeffrey L. Mendenhall; Rocco Moretti; Jens Meiler; Daniel Cremers (CoRR, 2020)

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs. - Brian Joseph Bender; Brennica Marlow; Jens Meiler (PLoS Comput. Biol., 2020)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

Multi-state design of flexible proteins predicts sequences optimal for conformational change. - Marion F. Sauer; Alexander M. Sevy; James E. Crowe Jr.; Jens Meiler (PLoS Comput. Biol., 2020)

General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. - Benjamin P. Brown; Jeffrey L. Mendenhall; Alexander R. Geanes; Jens Meiler (J. Chem. Inf. Model., 2021)

BCL: : Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. - Jeffrey L. Mendenhall; Benjamin P. Brown; Sandeepkumar Kothiwale; Jens Meiler (J. Chem. Inf. Model., 2021)

Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints. - Diego del Alamo; Kevin L. Jagessar; Jens Meiler; Hassane S. Mchaourab (PLoS Comput. Biol., 2021)

Computational redesign of a fluorogen activating protein with Rosetta. - Nina G. Bozhanova; Joel M. Harp; Brian Joseph Bender; Alexey S. Gavrikov; Dmitry A. Gorbachev; Mikhail S. Baranov; Christina B. Mercado; Xuan Zhang; Konstantin A. Lukyanov; Alexander S. Mishin; Jens Meiler (PLoS Comput. Biol., 2021)

Prediction of amphipathic helix - membrane interactions with Rosetta. - Alican Gulsevin; Jens Meiler (PLoS Comput. Biol., 2021)

Rosetta design with co-evolutionary information retains protein function. - Samuel Schmitz; Moritz Ertelt; Rainer Merkl; Jens Meiler (PLoS Comput. Biol., 2021)

Predicting the functional impact of KCNQ1 variants with artificial neural networks. - Saksham Phul; Georg Kuenze; Carlos G. Vanoye; Charles R. Sanders; Alfred L. George Jr.; Jens Meiler (PLoS Comput. Biol., 2022)

Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. - Marion F. S. Fischer; James E. Crowe Jr.; Jens Meiler (PLoS Comput. Biol., 2022)

Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery. - Yunchao Liu 001; Yu Wang 160; Oanh Vu; Rocco Moretti; Bobby Bodenheimer; Jens Meiler; Tyler Derr (AAAI, 2023)

Docking cholesterol to integral membrane proteins with Rosetta. - Brennica Marlow; Georg Kuenze; Jens Meiler; Julia Koehler Leman (PLoS Comput. Biol., 2023)

WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking. - Yunchao Liu 001; Ha Dong; Xin Wang 061; Rocco Moretti; Yu Wang 160; Zhaoqian Su; Jiawei Gu; Bobby Bodenheimer; Charles David Weaver; Jens Meiler; Tyler Derr (NeurIPS, 2024)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

Recent Advances in Automated Structure-Based De Novo Drug Design. - Yidan Tang; Rocco Moretti; Jens Meiler (J. Chem. Inf. Model., 2024)

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. - Moritz Ertelt; Vikram Khipple Mulligan; Jack B. Maguire; Sergey Lyskov; Rocco Moretti; Torben Schiffner; Jens Meiler; Clara T. Schoeder (PLoS Comput. Biol., 2024)

Interpretable Deep-Learning pKa Prediction for Small Molecule Drugs via Atomic Sensitivity Analysis. - Joseph Decorte; Benjamin P. Brown; Rathmell Jeffrey; Jens Meiler (J. Chem. Inf. Model., 2025)

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. - Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar Emilio Arrúa Arce; Roly J. Armstrong; Cheryl H. Arrowsmith; Kelly E. Bachta; Hartmut Beck; Dénes Berta; Mateusz K. Bieniek; et al. (J. Chem. Inf. Model., 2025)

Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors. - Yunchao Liu 001; Rocco Moretti; Yu Wang 160; Ha Dong; Bailu Yan; Bobby Bodenheimer; Tyler Derr; Jens Meiler (J. Chem. Inf. Model., 2025)

RosettaAMRLD: A Reaction-Driven Approach for Structure-Based Drug Design from Combinatorial Libraries with Monte Carlo Metropolis Algorithms. - Yidan Tang; Rocco Moretti; Jens Meiler (J. Chem. Inf. Model., 2025)

Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design. - Alexander Zlobin; Valentina D. Maslova; Julia Beliaeva; Jens Meiler; Andrey V. Golovin (J. Chem. Inf. Model., 2025)

Multi-state Protein Design with DynamicMPNN. - Alex Abrudan; Sebastian Pujalte Ojeda; Chaitanya K. Joshi; Matthew Greenig; Felipe Engelberger; Alena Khmelinskaia; Jens Meiler; Michele Vendruscolo; Tuomas P. J. Knowles (CoRR, 2025)

Crossover operators for molecular graphs with an application to virtual drug screening. - Nico Domschke; Bruno J. Schmidt; Thomas Gatter; Richard Golnik; Paul Eisenhuth; Fabian Liessmann; Jens Meiler; Peter F. Stadler (J. Cheminformatics, 2025)

SuperMetal: a generative AI framework for rapid and precise metal ion location prediction in proteins. - Xiaobo Lin; Zhaoqian Su; Yunchao Liu 001; Jingxian Liu; Xiaohan Kuang; Peter T. Cummings; Jesse Spencer-Smith; Jens Meiler (J. Cheminformatics, 2025)