Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Autonomous discovery in the chemical sciences part I: Progress

CW Coley, NS Eyke, KF Jensen - … Chemie International Edition, 2020 - Wiley Online Library
This two‐part Review examines how automation has contributed to different aspects of
discovery in the chemical sciences. In this first part, we describe a classification for …

Artificial intelligence, values, and alignment

I Gabriel - Minds and machines, 2020 - Springer
This paper looks at philosophical questions that arise in the context of AI alignment. It
defends three propositions. First, normative and technical aspects of the AI alignment …

Error estimates for deeponets: A deep learning framework in infinite dimensions

S Lanthaler, S Mishra… - … of Mathematics and Its …, 2022 - academic.oup.com
DeepONets have recently been proposed as a framework for learning nonlinear operators
map** between infinite-dimensional Banach spaces. We analyze DeepONets and prove …

MAFFT-DASH: integrated protein sequence and structural alignment

J Rozewicki, S Li, KM Amada, DM Standley… - Nucleic acids …, 2019 - academic.oup.com
Here, we describe a web server that integrates structural alignments with the MAFFT
multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based …

Improved protein structure prediction using predicted interresidue orientations

J Yang, I Anishchenko, H Park, Z Peng… - Proceedings of the …, 2020 - pnas.org
The prediction of interresidue contacts and distances from coevolutionary data using deep
learning has considerably advanced protein structure prediction. Here, we build on these …

Modeling aspects of the language of life through transfer-learning protein sequences

M Heinzinger, A Elnaggar, Y Wang, C Dallago… - BMC …, 2019 - Springer
Background Predicting protein function and structure from sequence is one important
challenge for computational biology. For 26 years, most state-of-the-art approaches …

Estimates on the generalization error of physics-informed neural networks for approximating a class of inverse problems for PDEs

S Mishra, R Molinaro - IMA Journal of Numerical Analysis, 2022 - academic.oup.com
Physics-informed neural networks (PINNs) have recently been very successfully applied for
efficiently approximating inverse problems for partial differential equations (PDEs). We focus …

Machine learning in enzyme engineering

S Mazurenko, Z Prokop, J Damborsky - ACS catalysis, 2019 - ACS Publications
Enzyme engineering plays a central role in develo** efficient biocatalysts for
biotechnology, biomedicine, and life sciences. Apart from classical rational design and …

Estimates on the generalization error of physics-informed neural networks for approximating PDEs

S Mishra, R Molinaro - IMA Journal of Numerical Analysis, 2023 - academic.oup.com
Physics-informed neural networks (PINNs) have recently been widely used for robust and
accurate approximation of partial differential equations (PDEs). We provide upper bounds …