Author: Kresten Lindorff-Larsen

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Preprints

FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries

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A structural biology community assessment of AlphaFold 2 applications

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Computing, analyzing and comparing the radius of gyration and hydrodynamic radius in conformational ensembles of intrinsically disordered proteins

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Rapid protein stability prediction using deep learning representations

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Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach

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Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation

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Accurate model of liquid-liquid phase behaviour of intrinsically-disordered proteins from data-driven optimization of single-chain properties

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Predicting and interpreting large scale mutagenesis data using analyses of protein stability and conservation

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Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

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Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories

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How well do force fields capture the strength of salt bridges in proteins?

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Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone

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Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance

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Deep mutational scanning by FACS-sorting of encapsulated E. coli micro-colonies

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Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop

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Global analysis of protein stability by temperature and chemical denaturation

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Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

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Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts

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Improving Martini 3 for disordered and multidomain proteins

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Global analysis of multi-mutants to improveprotein function

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Classifying disease-associated variants using measures of protein activity and stability

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Discovering functionally important sites in proteins

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A dual-reporter system for investigating and optimizing protein translation and folding in E. coli

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Cryo-EM structure of the human NKCC1 transporter reveals mechanisms of ion coupling and specificity

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Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

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Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

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Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase

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HSP70-binding motifs function as protein quality control degrons

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A comprehensive map of human glucokinase variant activity

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Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in the activation domain of a transcription factor

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PSX: Protein-Solvent Exchange - Software for calculation of deuterium-exchange effects in SANS measurements from protein coordinates

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Fitting side-chain NMR relaxation data using molecular simulations

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Order and disorder - an integrative structure of the full-length human growth hormone receptor

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Refinement of α-synuclein ensembles against SAXS data: Comparison of force fields and methods

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Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins

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Charge Interactions in a Highly Charge-depleted Protein

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Structural basis of client specificity in mitochondrial membrane-protein chaperones

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Refining conformational ensembles of flexible proteins against small-angle X-ray scattering data

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Interpreting the molecular mechanisms of disease variants in human membrane proteins

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Transient exposure of a buried phosphorylation site in an autoinhibited protein

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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

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Protein dynamics enables phosphorylation of buried residues in Cdk2/Cyclin A-bound p27

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Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

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Improved Predictions of Phase Behaviour of Intrinsically Disordered Proteins by Tuning the Interaction Range

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Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

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Conserved degronome features governing quality control-associated proteolysis

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Mg2+-dependent conformational equilibria in CorA: an integrated view on transport regulation

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Bayesian-Maximum-Entropy reweighting of IDP ensembles based on NMR chemical shifts

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Disease-linked mutations trigger exposure of a protein quality control degron in the DHFR protein

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Accurate protein stability predictions from homology models

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Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

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Prediction of quality-control degradation signals in yeast proteins

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DEER-PREdict: Software for Efficient Calculation of Spin-Labeling EPR and NMR Data from Conformational Ensembles

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Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

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Increasing protein stability by inferring substitution effects from high-throughput experiments

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Computational and experimental assessment of backbone templates for computational protein design

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Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

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NMR structures and functional roles of two related chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus

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Deciphering the alphabet of disorder -- Glu and Asp act differently on local but not global properties

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Evolutionarily conserved chaperone-mediated proteasomal degradation of a disease-linked aspartoacylase variant

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Synergistic stabilization of a double mutant in CI2 from an in-cell library screen

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Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

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Properdin oligomers adopt rigid extended conformations supporting function

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The prolactin receptor scaffolds Janus kinase 2 via co-structure formation with phosphoinositide-4,5-bisphosphate

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Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components

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WASCO: A Wasserstein-based statistical tool to compare conformational ensembles of intrinsically disordered proteins

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Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: comparison of experiments and computation.

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Slow conformational changes in the rigid and highly stable chymotrypsin inhibitor 2

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Rare catechol-O-methyltransferase (COMT) missense variants are structurally unstable proteasome targets

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