75 citations · 191 across the 12 of their papers we have counts for
14 papers
Detection of residual native state entropy changes upon mutation in Fyn SH3
Kresten Lindorff-Larsen, Robert B. Best, Anthony Mittermaier +3
NMR relaxation experiments have shown that there are small but measurable changes in the native state dynamics of the Fyn SH3 domain associated with the substitution by other amino…
Machine learning methods to study sequence-ensemble-function relationships in disordered proteins
Sören von Bülow, Giulio Tesei, Kresten Lindorff-Larsen
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, howe…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
Guidelines for releasing a variant effect predictor
Benjamin J. Livesey, Mihaly Badonyi, Mafalda Dias +15
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human geneti…
Diffusion of intrinsically disordered proteins within viscoelastic membraneless droplets
Fuga Watanabe, Takuma Akimoto, Robert B. Best +3
In living cells, intrinsically disordered proteins (IDPs), such as FUS and DDX4, undergo phase separation, forming biomolecular condensates. Using molecular dynamics simulations, w…
MolecularWebXR: Multiuser discussions about chemistry and biology in immersive and inclusive VR
Fabio J. Cortes Rodriguez, Gianfranco Frattini, Fernando Teixeira Pinto Meireles +6
MolecularWebXR is our new website for education, science communication and scientific peer discussion in chemistry and biology built on WebXR. It democratizes multi-user, inclusive…
Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins
F. Emil Thomasen, Kresten Lindorff-Larsen
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting…
On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins
Kresten Lindorff-Larsen, Birthe B. Kragelund
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) intersp…
Linking thermodynamics and measurements of protein stability
Kresten Lindorff-Larsen, Kaare Teilum
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary…
Dissecting the statistical properties of the Linear Extrapolation Method of determining protein stability
Kresten Lindorff-Larsen
When protein stability is measured by denaturant induced unfolding the linear extrapolation method is usually used to analyse the data. This method is based on the observation that…
What will computational modelling approaches have to say in the era of atomistic cryo-EM data?
James S. Fraser, Kresten Lindorff-Larsen, Massimiliano Bonomi
The focus of this viewpoint is to identify, in the era of atomistic resolution cryo-electron microscopy data, the areas in which computational modelling and molecular simulations w…
How to learn from inconsistencies: Integrating molecular simulations with experimental data
Simone Orioli, Andreas Haahr Larsen, Sandro Bottaro +1
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly us…
Frequency adaptive metadynamics for the calculation of rare-event kinetics
Yong Wang, Omar Valsson, Pratyush Tiwary +2
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predicti…
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
Anders S. Christensen, Troels E. Linnet, Mikael Borg +4
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that det…