Andrew M. Watkins

17 papers A* 2Journal 15
YearRankTypeTitle / Venue / Authors
2026 J jnl
Disentangling multispecific antibody function with graph neural networks.
CoRR
Joshua Southern, Changpeng Lu, Santrupti Nerli, Samuel Don Stanton, Andrew M. Watkins, Franziska Seeger, Frédéric A. Dreyer
2025 J jnl
Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins.
CoRR
Frédéric A. Dreyer, Jan Ludwiczak, Karolis Martinkus, Brennan Abanades, Robert G. Alberstein, Pan Kessel, Pranav Rao, Jae Hyeon Lee, Richard Bonneau, Andrew M. Watkins, Franziska Seeger
2025 J jnl
Unified all-atom molecule generation with neural fields.
CoRR
Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi
2024 J jnl
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms.
CoRR
Samuel Stanton, Robert G. Alberstein, Nathan C. Frey, Andrew M. Watkins, Kyunghyun Cho
2024 J jnl
LLMs are Highly-Constrained Biophysical Sequence Optimizers.
CoRR
Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2023 A* conf
3D molecule generation by denoising voxel grids.
NeurIPS
Pedro O. Pinheiro, Joshua A. Rackers, Joseph Kleinhenz, Michael Maser, Omar Mahmood, Andrew M. Watkins, Stephen Ra, Vishnu Sresht, Saeed Saremi
2023 J jnl
MoleCLUEs: Optimizing Molecular Conformers by Minimization of Differentiable Uncertainty.
CoRR
Michael Maser, Natasa Tagasovska, Jae Hyeon Lee, Andrew M. Watkins
2023 A* conf
OpenProteinSet: Training data for structural biology at scale.
NeurIPS
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
2023 J jnl
OpenProteinSet: Training data for structural biology at scale.
CoRR
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
2023 J jnl
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers.
CoRR
Michael Maser, Ji Won Park, Joshua Yao-Yu Lin, Jae Hyeon Lee, Nathan C. Frey, Andrew M. Watkins
2022 J jnl
Deep learning models for predicting RNA degradation via dual crowdsourcing.
Nat. Mac. Intell.
Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J. Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, Rhiju Das
2022 J jnl
Multi-segment preserving sampling for deep manifold sampler.
CoRR
Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
2022 J jnl
PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design.
CoRR
Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew M. Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
2021 J jnl
Predictive models of RNA degradation through dual crowdsourcing.
CoRR
Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J. Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, Anthony Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, Eterna Participants, Rhiju Das
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
2016 J jnl
Accurate
Nat.
Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker
2013 J jnl
HippDB: a database of readily targeted helical protein-protein interactions.
Bioinform.
Christina M. Bergey, Andrew M. Watkins, Paramjit S. Arora