Ingemar André

DECODING SYNONYMOUS CODON SELECTION WITH A TRANSFORMER MODEL

The paper develops a transformer model to predict codon sequences from amino acids, improving rare codon prediction and linking sequence variation to protein function.

Ancient amino acid sets enable stable protein folds

The paper designs ancient proteins using a limited amino acid set and shows they are stable and mutation-resilient.

Effects of single synonymous substitutions on folding efficiency demonstrate the influence of rare codons and protein structure

The paper investigates how single synonymous substitutions affect protein folding efficiency in E. coli, showing that rare codons and protein structure significantly influence this process.

Encoding of T=1 virus capsid structures through the interfaces of oligomer subcomponents

The paper analyzes protein-protein interfaces in T=1 virus capsids to determine their structural and energetic properties compared to non-viral homomers and their role in self-assembly.

Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

This paper combines AlphaFold with symmetric docking to accurately predict structures of symmetrical protein assemblies from sequence.

Atomistic simulation of protein evolution reveals sequence covariation and timedependent fluctuations of site-specific substitution rates

This study uses an all-atom simulator to show how fitness functions affect mutation rates and residue covariation in protein evolution.

A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and sidechain flexibility

This paper introduces EvoDOCK, a protein-protein docking algorithm that combines global search and local optimization to improve accuracy and speed using all-atom energy functions.

Linearised loop kinematics to study pathways between conformations

This paper introduces the JaLT algorithm to sample conformational transitions in protein loops, demonstrating its ability to generate realistic pathways and identify energy barriers in the MET20 loop of E. coli dihydrofolate reductase.