Improving Martini 3 for Disordered and Multidomain Proteins

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

(2022) F. Emil Thomasen et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles

(2021) Giulio Tesei et al.   PLoS Computational Biology

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

(2021) Erik W Martin et al.   NUCLEIC ACIDS RESEARCH

Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model

(2021) Ayan Majumder et al.   Journal of Chemical Theory and Computation

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

(2021) Christos Lamprakis et al.   Journal of Chemical Theory and Computation

Martini 3: a general purpose force field for coarse-grained molecular dynamics

(2021) Paulo C. T. Souza et al.   NATURE METHODS

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods

(2021) Mustapha Carab Ahmed et al.   Frontiers in Molecular Biosciences

Experimental noise in small-angle scattering can be assessed using the Bayesian indirect Fourier transformation

(2021) Andreas Haahr Larsen et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

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

(2021) Francesco Pesce et al.   BIOPHYSICAL JOURNAL

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

(2021) Giulio Tesei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

(2020) Jeong-Mo Choi et al.   Annual Review of Biophysics

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

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

(2020) Andreas Haahr Larsen et al.   PLoS Computational Biology

Conformational Ensembles of an Intrinsically Disordered Protein Consistent with NMR, SAXS, and Single-Molecule FRET

(2020) Gregory-Neal W. Gomes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The dynamics of linear polyubiquitin

(2020) Alexander Jussupow et al.   Science Advances

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

(2020) Zakarya Benayad et al.   Journal of Chemical Theory and Computation

The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions

(2020) Eric Fagerberg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Temperature Dependence of Intrinsically Disordered Proteins in Simulations: What are We Missing?

(2019) S. Jephthah et al.   Journal of Chemical Theory and Computation

Simulating and analysing configurational landscapes of protein–protein contact formation

(2019) Andrej Berg et al.   Interface Focus

Pitfalls of the Martini Model

(2019) Riccardo Alessandri et al.   Journal of Chemical Theory and Computation

Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression

(2019) Tiago N. Cordeiro et al.   STRUCTURE

Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation

(2018) Veronica H. Ryan et al.   MOLECULAR CELL

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

(2017) Joshua A. Riback et al.   SCIENCE

Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

(2017) Sergei Grudinin et al.   Acta Crystallographica Section D-Structural Biology

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

p15PAF Is an Intrinsically Disordered Protein with Nonrandom Structural Preferences at Sites of Interaction with Other Proteins

(2014) Alfredo De Biasio et al.   BIOPHYSICAL JOURNAL

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

(2014) Iren Wang et al.   NUCLEIC ACIDS RESEARCH

Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

(2013) Austin C. Stark et al.   Journal of Chemical Theory and Computation

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

The power of coarse graining in biomolecular simulations

(2013) Helgi I. Ingólfsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Noncovalent Dimerization of Ubiquitin

(2011) Zhu Liu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Metastasis-Associated Extracellular Matrix Protein Osteopontin Forms Transient Structure in Ligand Interaction Sites

(2011) Gerald Platzer et al.   BIOCHEMISTRY

Rotamer libraries of spin labelled cysteines for protein studies

(2010) Yevhen Polyhach et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Temperature-dependent structural changes in intrinsically disordered proteins: Formation of α-helices or loss of polyproline II?

(2010) Magnus Kjaergaard et al.   PROTEIN SCIENCE

Structural Polymorphism of 441-Residue Tau at Single Residue Resolution

(2009) Marco D Mukrasch et al.   PLOS BIOLOGY

Domain Conformation of Tau Protein Studied by Solution Small-Angle X-ray Scattering†

(2008) Efstratios Mylonas et al.   BIOCHEMISTRY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation