Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations

Bayesian methods in integrative structure modeling

(2023) Michael Habeck   BIOLOGICAL CHEMISTRY

Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach

(2021) Andrea Arsiccio et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations

(2021) Mattia Bernetti et al.   EUROPEAN PHYSICAL JOURNAL B

High Conformational Flexibility of the E2F1/DP1/DNA Complex

(2021) Dana Saad et al.   JOURNAL OF MOLECULAR BIOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case

(2021) Cristina Paissoni et al.   Frontiers in Molecular Biosciences

Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS

(2021) Samuel Naudi-Fabra et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Determination of protein structural ensembles by hybrid-resolution SAXS restrained Molecular Dynamics.

(2020) Cristina Paissoni et al.   Journal of Chemical Theory and Computation

Beamline B21: high-throughput small-angle X-ray scattering at Diamond Light Source

(2020) Nathan P. Cowieson et al.   JOURNAL OF SYNCHROTRON RADIATION

The dynamics of linear polyubiquitin

(2020) Alexander Jussupow et al.   Science Advances

Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data

(2019) Cristina Paissoni et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant

(2019) Toni Giorgino et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Promoting transparency and reproducibility in enhanced molecular simulations

(2019)   NATURE METHODS

The role of gelsolin domain 3 in familial amyloidosis (Finnish type)

(2019) Habiba Zorgati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion

(2019) Michela Bollati et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties

(2019) Matteo de Rosa et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin

(2019) Shuichi Takeda et al.   JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Interpreting solution X-ray scattering data using molecular simulations

(2018) Jochen S Hub   CURRENT OPINION IN STRUCTURAL BIOLOGY

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

(2018) Riccardo Capelli et al.   JOURNAL OF CHEMICAL PHYSICS

Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1

(2018) Hamed Kooshapur et al.   Nature Communications

Plasma Gelsolin: Indicator of Inflammation and Its Potential as a Diagnostic Tool and Therapeutic Target

(2018) Ewelina Piktel et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting

(2018) Ramya Rangan et al.   Journal of Chemical Theory and Computation

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

Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons

(2017) Anne T. Tuukkanen et al.   IUCrJ

ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions

(2017) D. Franke et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Accuracy limit of rigid 3-point water models

(2016) Saeed Izadi et al.   JOURNAL OF CHEMICAL PHYSICS

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement

(2016) Andrea Cesari et al.   Journal of Chemical Theory and Computation

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS

(2016) Mikayel Aznauryan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins

(2015) Alexey G. Kikhney et al.   FEBS LETTERS

Bayesian ensemble refinement by replica simulations and reweighting

(2015) Gerhard Hummer et al.   JOURNAL OF CHEMICAL PHYSICS

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

(2015) Christopher J. Knight et al.   NUCLEIC ACIDS RESEARCH

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

(2014) Po-chia Chen et al.   BIOPHYSICAL JOURNAL

SASBDB, a repository for biological small-angle scattering data

(2014) Erica Valentini et al.   NUCLEIC ACIDS RESEARCH

MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins

(2014) Stephan Niebling et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Gelsolin: The tail of a molecular gymnast

(2013) Shalini Nag et al.   Cytoskeleton

Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes

(2013) Krishnakumar M. Ravikumar et al.   JOURNAL OF CHEMICAL PHYSICS

Determining the phase diagram of water from direct coexistence simulations: The phase diagram of the TIP4P/2005 model revisited

(2013) M. M. Conde et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

(2013) Andrea Cavalli et al.   JOURNAL OF CHEMICAL PHYSICS

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Atomic-resolution structural information from scattering experiments on macromolecules in solution

(2013) Jürgen Köfinger et al.   PHYSICAL REVIEW E

Gelsolin amyloidosis: genetics, biochemistry, pathology and possible strategies for therapeutic intervention

(2012) James P. Solomon et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell

(2011) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

(2011) J. Bernauer et al.   RNA

Small-angle neutron scattering and contrast variation: a powerful combination for studying biological structures

(2010) William T. Heller   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

(2010) Kasper Stovgaard et al.   BMC BIOINFORMATICS

Multifunctional roles of gelsolin in health and diseases

(2010) Guo Hua Li et al.   MEDICINAL RESEARCH REVIEWS

FoXS: a web server for rapid computation and fitting of SAXS profiles

(2010) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

A Rapid Coarse Residue-Based Computational Method for X-Ray Solution Scattering Characterization of Protein Folds and Multiple Conformational States of Large Protein Complexes

(2009) Sichun Yang et al.   BIOPHYSICAL JOURNAL

Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin

(2009) S. Nag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA conformations and their sequence preferences

(2008) Daniel Svozil et al.   NUCLEIC ACIDS RESEARCH