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Karsten D. Householder

dblp:413/9516 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › protein design
inverse protein folding
0.912025
Predicting mutational effects on protein binding from folding energy · ICML 2025
Bioinformatics and computational biology › protein sequence analysis
protein sequence modeling
0.912025
Predicting mutational effects on protein binding from folding energy · ICML 2025

Methods — techniques the papers use, named apart from their topics

transfer learning · 0.9pre-trained inverse-folding model · 0.9deep learning · 0.9
YearPublicationVenuePosition
2025 Predicting mutational effects on protein binding from folding energy
abstract
Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed, but, presumably due to the scarcity of binding data, these methods underperform computationally expensive estimates based on empirical force fields. In response, we propose a transfer-learning approach that leverages advances in protein sequence modeling and folding stability prediction for this task. The key idea is to parameterize the binding energy as the difference between the folding energy of the protein complex and the sum of the folding energies of its binding partners. We show that using a pre-trained inverse-folding model as a proxy for folding energy provides strong zero-shot performance, and can be fine-tuned with (1) copious folding energy measurements and (2) more limited binding energy measurements. The resulting predictor, StaB-ddG, is the first deep learning predictor to match the accuracy of the state-of-the-art empirical force-field method FoldX, while offering an over 1,000x speed-up.
Arthur Deng, Karsten D. Householder, Fang Wu 0002, K. Christopher Garcia, Brian L. Trippe
ICML2