The complete list of my publications is available here.



Protein sequence-to-structure learning: Is this the end (-to-end revolution)?

E. Laine, S. Eismann, A. Elofsson, S. Grudinin - equal contributions (2021) Proteins - in press
We provide CASP participants and observers with some overview of the recent developments in deep learning applied to protein structure prediction, and some comprehensive description of key concepts we think have contributed to the formidable improvements we have witnessed in the latest CASP edition. We also discuss the implications of these improvements, the next-to-solve problems, and speculate about the future of structural (and computational) biology. View details »

Assessing conservation of alternative splicing with evolutionary splicing graphs

D.J. Zea, S. Laskina, A. Baudin, H. Richard* and E. Laine* (2021) Genome Research
We introduce a new concept and provide a practical solution to assess alternative splicing evolutionary conservation. We show a clear link between functional relevance, conservation and tissue regulation of alternative transcripts. We validated our method on a new set of 50 genes and scaled its application to the whole human protein-coding genome. We show that alternative usage of pseudo-repeats is not a rare phenomenon. You may browse the results here. View details »

A global metagenomic map of urban microbiomes and antimicrobial resistance

D. Danko et al. (2021) Cell
We present a global atlas of almost 5,000 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. View details »

HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps

E. Laine* and S. Grudinin* (2021) The Journal of Physical Chemistry B
In light of the recent very rapid progress in protein structure prediction, accessing the multitude of functional protein states is becoming more central than ever before. We have developed HOPMA, a novel method to predict protein functional states and transitions by using a modified elastic network model. HOPMA exploits patterns in a protein contact map, taking its 3D structure as input, and excludes some disconnected patches from the elastic network. Combined with nonlinear normal mode analysis, this strategy boosts the protein conformational space exploration, especially when the input structure is highly constrained, as we demonstrate on a set of more than 400 transitions. View details »

Targeting Solute Carrier Transporters through Functional Mapping

C. Colas and E. Laine (2020) Trends in Pharmacological Sciences
Solute carrier (SLC) transporters are emerging drug targets. Identifying the molecular determinants responsible for their specific and selective transport activities and describing key interactions with their ligands are crucial steps towards the design of potential new drugs. We provide a perspective and a general call to the scientific community to create a systematic roadmap for characterizing the SLC superfamily, in the context of drug discovery, structure and function. We propose that integrative approaches combining structure and sequence information would yield a predictive functional map and help to design molecules modulating cellular transport. View details »

Predicting substitutions to modulate disorder and stability in coiled-coils

Y. Karami, P. Saighi, R. Vanderhaegen, D. Gerlier, S. Longhi, E. Laine* and A. Carbone* (2020) BMC bioinformatics
We propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV). We derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. View details »