Jens Meiler

Publication Activity (10 Years)

Years Active: 2000-2023
Publications (10 Years): 32

Top Topics

Quantitative Structure Activity

Top Venues

PLoS Comput. Biol.

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

Publications

Yunchao Liu, Yu Wang, Oanh Vu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler, Tyler Derr
Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery. AAAI (2023)
Brennica Marlow, Georg Kuenze, Jens Meiler, Julia Koehler Leman
Docking cholesterol to integral membrane proteins with Rosetta. PLoS Comput. Biol. 19 (3) (2023)
Marion F. S. Fischer, James E. Crowe Jr., Jens Meiler
Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. PLoS Comput. Biol. 18 (12) (2022)
Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George Jr., Jens Meiler
Predicting the functional impact of KCNQ1 variants with artificial neural networks. PLoS Comput. Biol. 18 (4) (2022)
Benjamin P. Brown, Jeffrey L. Mendenhall, Alexander R. Geanes, Jens Meiler
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. J. Chem. Inf. Model. 61 (2) (2021)
Nina G. Bozhanova, Joel M. Harp, Brian J. Bender, Alexey S. Gavrikov, Dmitry A. Gorbachev, Mikhail S. Baranov, Christina B. Mercado, Xuan Zhang, Konstantin A. Lukyanov, Alexander S. Mishin, Jens Meiler
Computational redesign of a fluorogen activating protein with Rosetta. PLoS Comput. Biol. 17 (11) (2021)
Diego del Alamo, Kevin L. Jagessar, Jens Meiler, Hassane S. Mchaourab
Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints. PLoS Comput. Biol. 17 (6) (2021)
Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler
Rosetta design with co-evolutionary information retains protein function. PLoS Comput. Biol. 17 (1) (2021)
Alican Gulsevin, Jens Meiler
Prediction of amphipathic helix - membrane interactions with Rosetta. PLoS Comput. Biol. 17 (3) (2021)
Jeffrey L. Mendenhall, Benjamin P. Brown, Sandeepkumar Kothiwale, Jens Meiler
BCL: : Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. J. Chem. Inf. Model. 61 (1) (2021)
Marion F. Sauer, Alexander M. Sevy, James E. Crowe Jr., Jens Meiler
Multi-state design of flexible proteins predicts sequences optimal for conformational change. PLoS Comput. Biol. 16 (2) (2020)
Brian Joseph Bender, Brennica Marlow, Jens Meiler
Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs. PLoS Comput. Biol. 16 (10) (2020)
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, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16 (5) (2020)
Vladimir Golkov, Alexander Becker, Daniel T. Plop, Daniel Cuturilo, Neda Davoudi, Jeffrey L. Mendenhall, Rocco Moretti, Jens Meiler, Daniel Cremers
Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions. CoRR (2020)
Yunchao Liu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler
Foldit Drug Design Game Usability Study: Comparison of Citizen and Expert Scientists. MIG (2020)
Vladimir Golkov, Marcin J. Skwark, Atanas Mirchev, Georgi Dikov, Alexander R. Geanes, Jeffrey L. Mendenhall, Jens Meiler, Daniel Cremers
3D Deep Learning for Biological Function Prediction from Physical Fields. 3DV (2020)
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.
PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. BMC Bioinform. 21 (1) (2020)
Benjamin P. Brown, Jeffrey L. Mendenhall, Jens Meiler
BCL: : MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping. J. Chem. Inf. Model. 59 (2) (2019)
Alexander M. Sevy, Cinque S. Soto, Robin G. Bombardi, Jens Meiler, James E. Crowe Jr.
Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures. BMC Bioinform. 20 (1) (2019)
Oanh Vu, Jeffrey L. Mendenhall, Doaa Altarawy, Jens Meiler
BCL: : Mol2D - a robust atom environment descriptor for QSAR modeling and lead optimization. J. Comput. Aided Mol. Des. 33 (5) (2019)
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
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. BMC Bioinform. 19 (1) (2018)
Darwin Y. Fu, Jens Meiler
Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. J. Chem. Inf. Model. 58 (2) (2018)
Steven A. Combs, Benjamin K. Mueller, Jens Meiler
Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. J. Chem. Inf. Model. 58 (5) (2018)
Alexander M. Sevy, Swetasudha Panda, James E. Crowe Jr., Jens Meiler, Yevgeniy Vorobeychik
Integrating linear optimization with structural modeling to increase HIV neutralization breadth. PLoS Comput. Biol. 14 (2) (2018)
Vladimir Golkov, Marcin J. Skwark, Atanas Mirchev, Georgi Dikov, Alexander R. Geanes, Jeffrey L. Mendenhall, Jens Meiler, Daniel Cremers
3D Deep Learning for Biological Function Prediction from Physical Fields. CoRR (2017)
Francois Berenger, Oanh Vu, Jens Meiler
Consensus queries in ligand-based virtual screening experiments. J. Cheminformatics 9 (1) (2017)
Jeffrey L. Mendenhall, Jens Meiler
Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout. J. Comput. Aided Mol. Des. 30 (2) (2016)
Gregory Sliwoski, Jeffrey L. Mendenhall, Jens Meiler
Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. J. Comput. Aided Mol. Des. 30 (3) (2016)
Bian Li, Jeffrey L. Mendenhall, Elizabeth Dong Nguyen, Brian E. Weiner, Axel W. Fischer, Jens Meiler
Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J. Chem. Inf. Model. 56 (2) (2016)
Vladimir Golkov, Marcin J. Skwark, Antonij Golkov, Alexey Dosovitskiy, Thomas Brox, Jens Meiler, Daniel Cremers
Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images. NIPS (2016)
Sandeepkumar Kothiwale, Jeffrey L. Mendenhall, Jens Meiler
BCL: : Conf: small molecule conformational sampling using a knowledge based rotamer library. J. Cheminformatics 7 (2015)
Alexander M. Sevy, Tim M. Jacobs, James E. Crowe Jr., Jens Meiler
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. PLoS Comput. Biol. 11 (7) (2015)
Steffen Lindert, Phoebe L. Stewart, Jens Meiler
Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Comput. Biol. Chem. 42 (2013)
Joseph J. Crivelli, Gordon Lemmon, Kristian Kaufmann, Jens Meiler
Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. J. Comput. Aided Mol. Des. 27 (12) (2013)
Jordan R. Willis, Bryan S. Briney, Samuel L. DeLuca, James E. Crowe Jr., Jens Meiler
Human Germline Antibody Gene Segments Encode Polyspecific Antibodies. PLoS Comput. Biol. 9 (4) (2013)
Edward W. Lowe, Mariusz Butkiewicz, Nils Woetzel, Jens Meiler
GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data. CIBCB (2012)
Mariusz Butkiewicz, Edward W. Lowe, Jens Meiler
Bcl∷ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimer's Disease. CIBCB (2012)
Edward W. Lowe, Nils Woetzel, Jens Meiler
Poster: GPU-accelerated artificial neural network for QSAR modeling. ICCABS (2011)
Nathan Alexander, Nils Woetzel, Jens Meiler
Bcl: : Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System. ICCABS (2011)
Edward W. Lowe, Mariusz Butkiewicz, Matthew Spellings, Albert Omlor, Jens Meiler
Comparative analysis of machine learning techniques for the prediction of logP. CIBCB (2011)
Edward W. Lowe, Nils Woetzel, Jens Meiler
Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps. ICCABS (2011)
Mert Karakas, Nils Woetzel, Jens Meiler
Structure Determination. J. Comput. Biol. 17 (2) (2010)
Mariusz Butkiewicz, Ralf Mueller, Danilo Selic, Eric Dawson, Jens Meiler
Application of machine learning approaches on quantitative structure activity relationships. CIBCB (2009)
Gregory D. Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler, Tanja Kortemme
A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family. PLoS Comput. Biol. 5 (5) (2009)
Julia Koehler, Ralf Mueller, Jens Meiler
Improved prediction of trans-membrane spans in proteins using an artificial neural network. CIBCB (2009)
Kristian Kaufmann, Jens Meiler
Small Molecules as Rotamers: Generation and Docking in RosettaLigand. German Conference on Bioinformatics (2008)
Jens Meiler, Erdogan Sanli, Jochen Junker, Reinhard Meusinger, Thomas Lindel, Martin Will, Walter Maier, Matthias Köck
Validation of Structural Proposals by Substructure Analysis and 13C NMR Chemical Shift Prediction. J. Chem. Inf. Comput. Sci. 42 (2) (2002)
Jens Meiler, Martin Will
Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks. J. Chem. Inf. Comput. Sci. 41 (6) (2001)
Jens Meiler, Reinhard Meusinger, Martin Will
Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks. J. Chem. Inf. Comput. Sci. 40 (5) (2000)