Jens Meiler - RankMe

66 papers A* 2C 6Journal 52Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2. J. Chem. Inf. Model. Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl H. Arrowsmith, Alan Ashworth, Fuqiang Ban, Hartmut Beck, Kevin P. Bishop, Hugo J. Bohórquez, Albina Bolotokova, Marko Breznik, Irene Chau, Yu Chen, Artem Cherkasov, Wim Dehaen, Dennis Della Corte, Katrin Denzinger, Niklas Piet Doering, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Francesco Gentile, Elisa Gibson, Ozan Gökdemir, Anders Gunnarsson, Judith Guenther, John J. Irwin, Jan Halborg Jensen, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Ashley Hutchinson, Shubhangi Kandwal, Andrea Karlova, Kushal Koirala, Sergei Kotelnikov, Dima Kozakov, Juyong Lee, Soowon Lee, Uta F. Lessel, Sijie Liu, Xuefeng Liu, Peter Loppnau, Jens Meiler, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Tudor I. Oprea, Brooks Paige, Amit Pandit, Keunwan Park, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Rahul Ravichandran, Didier Rognan, Edina Rosta, Yogesh Sabnis, Thomas Scott, Almagul Seitova, Purshotam Sharma, François Sindt, Minghu Song, Casper Steinmann, Rick Stevens, Valerij Talagayev, Valentyna V. Tararina, Olga O. Tarkhanova, Damon Tingey, John F. Trant, Dakota Treleaven, Alexander Tropsha, W. Patrick Walters, Jude Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Shuangjia Zheng, James S. Fraser, Matthieu Schapira
2025	J	`jnl`	Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors. J. Chem. Inf. Model. Yunchao Liu, Rocco Moretti, Yu Wang, Ha Dong, Bailu Yan, Bobby Bodenheimer, Tyler Derr, Jens Meiler
2025	J	`jnl`	CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. J. Chem. Inf. Model. 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, Vincent Blay, Albina Bolotokova, Philip E. Bourne, Marko Breznik, Peter J. Brown, Aaron D. G. Campbell, Emanuele Carosati, Irene Chau, Daniel J. Cole, Ben Cree, Wim Dehaen, Katrin Denzinger, Karina dos Santos Machado, Ian Dunn, Prasannavenkatesh Durai, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Daniel Felfoldi, Kallie Friston, Pegah Ghiabi, Elisa Gibson, Judith Guenther, Anders Gunnarsson, Alexander Hillisch, Douglas R. Houston, Jan Halborg Jensen, Rachel J. Harding, Kate S. Harris, Laurent Hoffer, Anders Hogner, Joshua T. Horton, Scott Houliston, Judd F. Hultquist, Ashley Hutchinson, John J. Irwin, Marko Jukic, Shubhangi Kandwal, Andrea Karlova, Vittorio L. Katis, Ryan P. Kich, Dmitri Kireev, David Koes, Nicole L. Inniss, Uta F. Lessel, Sijie Liu, Peter Loppnau, Wei Lu, Sam Alexander Martino, Miles McGibbon, Jens Meiler, Akhila Mettu, Sam Money-Kyrle, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Joseph A. Newman, Leon Obendorf, Brooks Paige, Amit Pandit, Keunwan Park, Sumera Perveen, Rachael Pirie, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Federico Ricci, Natalie J. Roper, Edina Rosta, Margarita Rzhetskaya, Yogesh Sabnis, Karla J. F. Satchell, Frederico Schmitt Kremer, Thomas Scott, Almagul Seitova, Casper Steinmann, Valerij Talagayev, Olga O. Tarkhanova, Natalie J. Tatum, Dakota Treleaven, Adriano Velasque Werhli, W. Patrick Walters, Xiaowen Wang, Jude Wells, Geoffrey Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Jixian Zhang, Zheng Zhao, Shuangjia Zheng, Matthieu Schapira
2025	J	`jnl`	Cache: Utilizing ultra-large library screening in Rosetta to identify novel binders of the WD-repeat domain of Leucine-Rich Repeat Kinase 2. J. Cheminformatics Fabian Liessmann, Paul Eisenhuth, Alexander Fuerll, Oanh Vu, Rocco Moretti, Jens Meiler
2025	J	`jnl`	Crossover operators for molecular graphs with an application to virtual drug screening. J. Cheminformatics Nico Domschke, Bruno J. Schmidt, Thomas Gatter, Richard Golnik, Paul Eisenhuth, Fabian Liessmann, Jens Meiler, Peter F. Stadler
2025	J	`jnl`	FakeRotLib: Expedient Noncanonical Amino Acid Parametrization in Rosetta. J. Chem. Inf. Model. Eric W. Bell, Benjamin P. Brown, Jens Meiler
2025	J	`jnl`	Interpretable Deep-Learning p J. Chem. Inf. Model. Joseph Decorte, Benjamin P. Brown, Rathmell Jeffrey, Jens Meiler
2025	J	`jnl`	Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design. J. Chem. Inf. Model. Alexander Zlobin, Valentina D. Maslova, Julia Beliaeva, Jens Meiler, Andrey V. Golovin
2025	J	`jnl`	Multi-state Protein Design with DynamicMPNN. CoRR Alex Abrudan, Sebastian Pujalte Ojeda, Chaitanya K. Joshi, Matthew Greenig, Felipe Engelberger, Alena Khmelinskaia, Jens Meiler, Michele Vendruscolo, Tuomas P. J. Knowles
2025	J	`jnl`	RosettaAMRLD: A Reaction-Driven Approach for Structure-Based Drug Design from Combinatorial Libraries with Monte Carlo Metropolis Algorithms. J. Chem. Inf. Model. Yidan Tang, Rocco Moretti, Jens Meiler
2025	J	`jnl`	Scaffold-Aware Generative Augmentation and Reranking for Enhanced Virtual Screening. CoRR Xin Wang, Yu Wang, Yunchao Liu, Jens Meiler, Tyler Derr
2025	J	`jnl`	SuperMetal: a generative AI framework for rapid and precise metal ion location prediction in proteins. J. Cheminformatics Xiaobo Lin, Zhaoqian Su, Yunchao Liu, Jingxian Liu, Xiaohan Kuang, Peter T. Cummings, Jesse Spencer-Smith, Jens Meiler
2024	J	`jnl`	CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. J. Chem. Inf. Model. 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, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled M. Edwards, Merveille K. I. Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S. Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J. Irwin, Olexandr Isayev, Aleksandra Ivanova, Célien Jacquemard, Austin J. Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta F. Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J. Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel G. Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina E. M. Schindler, François Sindt, Vojtech Spiwok, Casper Steinmann, Rick L. Stevens, Valerij Talagayev, Damon Tingey, Oanh Vu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, Matthieu Schapira
2024	J	`jnl`	Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. PLoS Comput. Biol. Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, Clara T. Schoeder
2024	J	`jnl`	Recent Advances in Automated Structure-Based De Novo Drug Design. J. Chem. Inf. Model. Yidan Tang, Rocco Moretti, Jens Meiler
2024	A*	`conf`	WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking. NeurIPS Yunchao Liu, Ha Dong, Xin Wang, Rocco Moretti, Yu Wang, Zhaoqian Su, Jiawei Gu, Bobby Bodenheimer, Charles David Weaver, Jens Meiler, Tyler Derr
2024	J	`jnl`	WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking. CoRR Yunchao Liu, Ha Dong, Xin Wang, Rocco Moretti, Yu Wang, Zhaoqian Su, Jiawei Gu, Bobby Bodenheimer, Charles David Weaver, Jens Meiler, Tyler Derr
2023	J	`jnl`	Docking cholesterol to integral membrane proteins with Rosetta. PLoS Comput. Biol. Brennica Marlow, Georg Kuenze, Jens Meiler, Julia Koehler Leman
2023	A*	`conf`	Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery. AAAI Yunchao Liu, Yu Wang, Oanh Vu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler, Tyler Derr
2022	J	`jnl`	Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods. PLoS Comput. Biol. Marion F. S. Fischer, James E. Crowe Jr., Jens Meiler
2022	J	`jnl`	Predicting the functional impact of KCNQ1 variants with artificial neural networks. PLoS Comput. Biol. Saksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George Jr., Jens Meiler
2021	J	`jnl`	BCL: : Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. J. Chem. Inf. Model. Jeffrey L. Mendenhall, Benjamin P. Brown, Sandeepkumar Kothiwale, Jens Meiler
2021	J	`jnl`	Computational redesign of a fluorogen activating protein with Rosetta. PLoS Comput. Biol. 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
2021	J	`jnl`	General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. J. Chem. Inf. Model. Benjamin P. Brown, Jeffrey L. Mendenhall, Alexander R. Geanes, Jens Meiler
2021	J	`jnl`	Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints. PLoS Comput. Biol. Diego del Alamo, Kevin L. Jagessar, Jens Meiler, Hassane S. Mchaourab
2021	J	`jnl`	Prediction of amphipathic helix - membrane interactions with Rosetta. PLoS Comput. Biol. Alican Gulsevin, Jens Meiler
2021	J	`jnl`	Rosetta design with co-evolutionary information retains protein function. PLoS Comput. Biol. Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler
2020	—	`conf`	3D Deep Learning for Biological Function Prediction from Physical Fields. 3DV Vladimir Golkov, Marcin J. Skwark, Atanas Mirchev, Georgi Dikov, Alexander R. Geanes, Jeffrey L. Mendenhall, Jens Meiler, Daniel Cremers
2020	J	`jnl`	Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 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
2020	J	`jnl`	Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions. CoRR Vladimir Golkov, Alexander Becker, Daniel T. Plop, Daniel Cuturilo, Neda Davoudi, Jeffrey L. Mendenhall, Rocco Moretti, Jens Meiler, Daniel Cremers
2020	C	`conf`	Foldit Drug Design Game Usability Study: Comparison of Citizen and Expert Scientists. MIG Yunchao Liu, Rocco Moretti, Bobby Bodenheimer, Jens Meiler
2020	J	`jnl`	Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs. PLoS Comput. Biol. Brian Joseph Bender, Brennica Marlow, Jens Meiler
2020	J	`jnl`	Multi-state design of flexible proteins predicts sequences optimal for conformational change. PLoS Comput. Biol. Marion F. Sauer, Alexander M. Sevy, James E. Crowe Jr., Jens Meiler
2020	J	`jnl`	PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. BMC Bioinform. 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.
2019	J	`jnl`	BCL: : Mol2D - a robust atom environment descriptor for QSAR modeling and lead optimization. J. Comput. Aided Mol. Des. Oanh Vu, Jeffrey L. Mendenhall, Doaa Altarawy, Jens Meiler
2019	J	`jnl`	BCL: : MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping. J. Chem. Inf. Model. Benjamin P. Brown, Jeffrey L. Mendenhall, Jens Meiler
2019	J	`jnl`	Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures. BMC Bioinform. Alexander M. Sevy, Cinque S. Soto, Robin G. Bombardi, Jens Meiler, James E. Crowe Jr.
2018	J	`jnl`	Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. J. Chem. Inf. Model. Steven A. Combs, Benjamin K. Mueller, Jens Meiler
2018	J	`jnl`	Integrating linear optimization with structural modeling to increase HIV neutralization breadth. PLoS Comput. Biol. Alexander M. Sevy, Swetasudha Panda, James E. Crowe Jr., Jens Meiler, Yevgeniy Vorobeychik
2018	J	`jnl`	Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. J. Chem. Inf. Model. Darwin Y. Fu, Jens Meiler
2018	J	`jnl`	Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. BMC Bioinform. 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
2017	J	`jnl`	3D Deep Learning for Biological Function Prediction from Physical Fields. CoRR Vladimir Golkov, Marcin J. Skwark, Atanas Mirchev, Georgi Dikov, Alexander R. Geanes, Jeffrey L. Mendenhall, Jens Meiler, Daniel Cremers
2017	J	`jnl`	Consensus queries in ligand-based virtual screening experiments. J. Cheminformatics Francois Berenger, Oanh Vu, Jens Meiler
2016	J	`jnl`	Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J. Chem. Inf. Model. Bian Li, Jeffrey L. Mendenhall, Elizabeth Dong Nguyen, Brian E. Weiner, Axel W. Fischer, Jens Meiler
2016	J	`jnl`	Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. J. Comput. Aided Mol. Des. Gregory Sliwoski, Jeffrey L. Mendenhall, Jens Meiler
2016	J	`jnl`	Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout. J. Comput. Aided Mol. Des. Jeffrey L. Mendenhall, Jens Meiler
2016	—	`conf`	Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images. NIPS Vladimir Golkov, Marcin J. Skwark, Antonij Golkov, Alexey Dosovitskiy, Thomas Brox, Jens Meiler, Daniel Cremers
2015	J	`jnl`	BCL: : Conf: small molecule conformational sampling using a knowledge based rotamer library. J. Cheminformatics Sandeepkumar Kothiwale, Jeffrey L. Mendenhall, Jens Meiler
2015	J	`jnl`	Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. PLoS Comput. Biol. Alexander M. Sevy, Tim M. Jacobs, James E. Crowe Jr., Jens Meiler
2013	J	`jnl`	Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Comput. Biol. Chem. Steffen Lindert, Phoebe L. Stewart, Jens Meiler
2013	J	`jnl`	Human Germline Antibody Gene Segments Encode Polyspecific Antibodies. PLoS Comput. Biol. Jordan R. Willis, Bryan S. Briney, Samuel L. DeLuca, James E. Crowe Jr., Jens Meiler
2013	J	`jnl`	Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. J. Comput. Aided Mol. Des. Joseph J. Crivelli, Gordon Lemmon, Kristian Kaufmann, Jens Meiler
2012	C	`conf`	Bcl∷ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimer's Disease. CIBCB Mariusz Butkiewicz, Edward W. Lowe, Jens Meiler
2012	C	`conf`	GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data. CIBCB Edward W. Lowe, Mariusz Butkiewicz, Nils Woetzel, Jens Meiler
2011	—	`conf`	Bcl: : Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System. ICCABS Nathan Alexander, Nils Woetzel, Jens Meiler
2011	C	`conf`	Comparative analysis of machine learning techniques for the prediction of logP. CIBCB Edward W. Lowe, Mariusz Butkiewicz, Matthew Spellings, Albert Omlor, Jens Meiler
2011	—	`conf`	Poster: GPU-accelerated artificial neural network for QSAR modeling. ICCABS Edward W. Lowe, Nils Woetzel, Jens Meiler
2011	—	`conf`	Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps. ICCABS Edward W. Lowe, Nils Woetzel, Jens Meiler
2010	J	`jnl`	BCL: : Contact-Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and J. Comput. Biol. Mert Karakas, Nils Woetzel, Jens Meiler
2009	J	`jnl`	A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family. PLoS Comput. Biol. Gregory D. Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler, Tanja Kortemme
2009	C	`conf`	Application of machine learning approaches on quantitative structure activity relationships. CIBCB Mariusz Butkiewicz, Ralf Mueller, Danilo Selic, Eric Dawson, Jens Meiler
2009	C	`conf`	Improved prediction of trans-membrane spans in proteins using an artificial neural network. CIBCB Julia Koehler, Ralf Mueller, Jens Meiler
2008	—	`conf`	Small Molecules as Rotamers: Generation and Docking in RosettaLigand. German Conference on Bioinformatics Kristian Kaufmann, Jens Meiler
2002	J	`jnl`	Validation of Structural Proposals by Substructure Analysis and 13C NMR Chemical Shift Prediction. J. Chem. Inf. Comput. Sci. Jens Meiler, Erdogan Sanli, Jochen Junker, Reinhard Meusinger, Thomas Lindel, Martin Will, Walter Maier, Matthias Köck
2001	J	`jnl`	Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra Using Genetic Algorithms and Neural Networks. J. Chem. Inf. Comput. Sci. Jens Meiler, Martin Will
2000	J	`jnl`	Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks. J. Chem. Inf. Comput. Sci. Jens Meiler, Reinhard Meusinger, Martin Will