Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble

(2018) Priscilla L. S. Boon et al.   ACS Chemical Biology

Femtosecond Hydration Map of Intrinsically Disordered α -Synuclein

(2018) Shruti Arya et al.   BIOPHYSICAL JOURNAL

Structure and Conformational Dynamics of the Human Spliceosomal B act Complex

(2018) David Haselbach et al.   CELL

Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy

(2018) Walter Becker et al.   CHEMPHYSCHEM

Molecular simulations of the ribosome and associated translation factors

(2018) Lars V Bock et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Interpreting solution X-ray scattering data using molecular simulations

(2018) Jochen S Hub   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding

(2018) Jungmin Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome

(2018) Lorenzo Casalino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of protein oligomeric structure from small-angle X-ray scattering

(2018) David A. Korasick et al.   PROTEIN SCIENCE

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

(2018) Przemyslaw Nogly et al.   SCIENCE

Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry

(2018) Joshua Matthew Allen Bullock et al.   STRUCTURE

Conformational States of ABC Transporter MsbA in a Lipid Environment Investigated by Small-Angle Scattering Using Stealth Carrier Nanodiscs

(2018) Inokentijs Josts et al.   STRUCTURE

Current Status of Single Particle Imaging with X-ray Lasers

(2018) Zhibin Sun et al.   Applied Sciences-Basel

Radiation Damage in Macromolecular Crystallography—An Experimentalist’s View

(2018) Helena Taberman   Crystals

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

(2018) Miki Nakano et al.   JOURNAL OF SYNCHROTRON RADIATION

Gaussian mixture model for coarse-grained modeling from XFEL

(2018) Tetsuro Nagai et al.   OPTICS EXPRESS

Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin

(2018) Suliman Adam et al.   PLoS One

Hydrogen–deuterium exchange reveals long-range dynamical allostery in soybean lipoxygenase

(2017) Adam R. Offenbacher et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations

(2017) Marcus Wieder et al.   Journal of Chemical Information and Modeling

Kinetics from Replica Exchange Molecular Dynamics Simulations

(2017) Lukas S. Stelzl et al.   Journal of Chemical Theory and Computation

Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

(2017) David Stelter et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Uncoupling of an ammonia channel as a mechanism of allosteric inhibition in anthranilate synthase of Serratia marcescens: dynamic and graph theoretical analysis

(2017) Ashutosh Srivastava et al.   Molecular BioSystems

Structure and dynamics of the RNAPII CTDsome with Rtt103

(2017) Olga Jasnovidova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ligand-induced conformational dynamics of theEscherichia coliNa+/H+antiporter NhaA revealed by hydrogen/deuterium exchange mass spectrometry

(2017) Martin Lorenz Eisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Water is an active matrix of life for cell and molecular biology

(2017) Philip Ball   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular ensembles make evolution unpredictable

(2017) Zachary R. Sailer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

(S)Pinning down protein interactions by NMR

(2017) Kaare Teilum et al.   PROTEIN SCIENCE

Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition

(2017) Ashutosh Srivastava et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

(2017) Joerg Schaarschmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

(2017) Stephen K. Burley et al.   STRUCTURE

A Bright Future for Serial Femtosecond Crystallography with XFELs

(2017) Linda C. Johansson et al.   TRENDS IN BIOCHEMICAL SCIENCES

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density

(2017) Nicholas M. Pearce et al.   Nature Communications

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate

(2017) Takehiko Tosha et al.   Nature Communications

An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences

(2017) Su Datt Lam 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

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase

(2017) Atsuhiro Shimada et al.   Science Advances

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

(2017) Logan S. Ahlstrom et al.   PLoS One

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Serial femtosecond crystallography: A revolution in structural biology

(2016) Jose M. Martin-Garcia et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The Current Revolution in Cryo-EM

(2016) Edward H. Egelman   BIOPHYSICAL JOURNAL

Structural Basis for Gating and Activation of RyR1

(2016) Amédée des Georges et al.   CELL

Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

(2016) Alan Merk et al.   CELL

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Recent excitements in protein NMR: Large proteins and biologically relevant dynamics

(2016) Sai Chaitanya Chiliveri et al.   JOURNAL OF BIOSCIENCES

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy

(2016) Lewis E. Kay   JOURNAL OF MOLECULAR BIOLOGY

Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns

(2016) Atsushi Tokuhisa et al.   JOURNAL OF STRUCTURAL BIOLOGY

The role of protein dynamics in the evolution of new enzyme function

(2016) Eleanor Campbell et al.   Nature Chemical Biology

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

(2016) Dina Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Computational investigation of cold denaturation in the Trp-cage miniprotein

(2016) Sang Beom Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the human 26S proteasome at a resolution of 3.9 Å

(2016) Andreas Schweitzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules

(2016) Rei Matsuoka et al.   PROTEIN SCIENCE

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

(2016) J. Kosinski et al.   SCIENCE

A three-dimensional movie of structural changes in bacteriorhodopsin

(2016) Eriko Nango et al.   SCIENCE

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

(2016) Alexander Leitner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

(2016) Isseki Yu et al.   eLife

Condor: a simulation tool for flash X-ray imaging

(2016) Max F. Hantke et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Comparing the intrinsic dynamics of multiple protein structures using elastic network models

(2015) Edvin Fuglebakk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

(2015) Matthew G. Quesne et al.   CHEMISTRY-A EUROPEAN JOURNAL

Dynamics Based Pharmacophore Models for Screening Potential Inhibitors of Mycobacterial Cyclopropane Synthase

(2015) Chinmayee Choudhury et al.   Journal of Chemical Information and Modeling

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

(2015) João Henriques et al.   Journal of Chemical Theory and Computation

Gating machinery of InsP3R channels revealed by electron cryomicroscopy

(2015) Guizhen Fan et al.   NATURE

Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

(2015) Raymond G Sierra et al.   NATURE METHODS

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

(2015) Frank DiMaio et al.   NATURE METHODS

Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser

(2015) Tomas Ekeberg et al.   PHYSICAL REVIEW LETTERS

Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy

(2015) Johanna Becker-Baldus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

(2015) Pawel A. Janowski et al.   PROTEIN SCIENCE

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

(2015) Andrej Sali et al.   STRUCTURE

Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

(2015) Giorgio Schirò et al.   Nature Communications

Radiation decay of thaumatin crystals at three X-ray energies

(2015) Dorothee Liebschner et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering

(2015) Giancarlo Tria et al.   IUCrJ

The linac coherent light source single particle imaging road map

(2015) A. Aquila et al.   Structural Dynamics

Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions

(2014) Christopher J. Oldfield et al.   Annual Review of Biochemistry

A Glimpse of Structural Biology through X-Ray Crystallography

(2014) Yigong Shi   CELL

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

(2014) Daniel J. Cole et al.   Journal of Chemical Theory and Computation

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

pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State

(2014) T. Dwight McGee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

New Insights into the Role of Water in Biological Function: Studying Solvated Biomolecules Using Terahertz Absorption Spectroscopy in Conjunction with Molecular Dynamics Simulations

(2014) Valeria Conti Nibali et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

(2014) R. B. Fenwick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Femtosecond Crystallography with Ultrabright Electrons and X-rays: Capturing Chemistry in Action

(2014) R. J. D. Miller   SCIENCE

Protein crystallography from the perspective of technology developments

(2014) Xiao-Dong Su et al.   Crystallography Reviews

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

(2014) Antonija Kuzmanic et al.   Nature Communications

Imaging live cell in micro-liquid enclosure by X-ray laser diffraction

(2014) Takashi Kimura et al.   Nature Communications

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins

(2014) P. Craveur et al.   Database-The Journal of Biological Databases and Curation

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

(2013) Edwin Pozharski et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Visualizing ligand molecules in twilight electron density

(2013) Christian X. Weichenberger et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology

(2013) Robert P. Rambo et al.   Annual Review of Biophysics

Structure of RDE-4 dsRBDs and mutational studies provide insights into dsRNA recognition in theCaenorhabditis elegansRNAi pathway

(2013) Sai Chaitanya Chiliveri et al.   BIOCHEMICAL JOURNAL

Molecular Model of a Soluble Guanylyl Cyclase Fragment Determined by Small-Angle X-ray Scattering and Chemical Cross-Linking

(2013) Bradley G. Fritz et al.   BIOCHEMISTRY

Water in Photosystem II: Structural, functional and mechanistic considerations

(2013) Katrin Linke et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Exploring the role of receptor flexibility in structure-based drug discovery

(2013) Ferran Feixas et al.   BIOPHYSICAL CHEMISTRY

A historical perspective on protein crystallization from 1840 to the present day

(2013) Richard Giegé   FEBS Journal

Exploring the effect of PARP-1 flexibility in docking studies

(2013) Albert A. Antolin et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Peptide Crystal Simulations Reveal Hidden Dynamics

(2013) Pawel A. Janowski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding

(2013) Benjamin Breiten et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

Improved low-resolution crystallographic refinement with Phenix and Rosetta

(2013) Frank DiMaio et al.   NATURE METHODS

Cross-Link Guided Molecular Modeling with ROSETTA

(2013) Abdullah Kahraman et al.   PLoS One

Packing interface energetics in different crystal forms of the λ Cro dimer

(2013) Logan S. Ahlstrom et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model

(2013) Shen Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Serial Femtosecond Crystallography of G Protein-Coupled Receptors

(2013) W. Liu et al.   SCIENCE

Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography

(2013) Xue Wang et al.   PLoS Pathogens

Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias

(2012) Karsten Klopffleisch et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Biological insights from hydrogen exchange mass spectrometry

(2012) Sheila S. Jaswal   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Protein Contact Networks: An Emerging Paradigm in Chemistry

(2012) L. Di Paola et al.   CHEMICAL REVIEWS

Protein Electrostatic Properties Predefining the Level of Surface Hydrophobicity Change upon Phosphorylation

(2012) Anton A. Polyansky et al.   Journal of Physical Chemistry Letters

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Allosteric post-translational modification codes

(2012) Ruth Nussinov et al.   TRENDS IN BIOCHEMICAL SCIENCES

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

(2011) Shina C.L. Kamerlin et al.   Annual Review of Physical Chemistry

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

(2011) Logan S. Ahlstrom et al.   BIOPHYSICAL JOURNAL

Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target

(2011) William Sinko et al.   Chemical Biology & Drug Design

Excited states of ribosome translocation revealed through integrative molecular modeling

(2011) P. C. Whitford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

(2010) P. Therese Lang et al.   PROTEIN SCIENCE

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

(2009) Henry van den Bedem et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Solution and Crystal Molecular Dynamics Simulation Study of m4-Cyanovirin-N Mutants Complexed with Di-Mannose

(2009) Ivan I. Vorontsov et al.   BIOPHYSICAL JOURNAL

Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps

(2009) Ivan Grubisic et al.   JOURNAL OF STRUCTURAL BIOLOGY

A beginner's guide to radiation damage

(2009) James M. Holton   JOURNAL OF SYNCHROTRON RADIATION

What recent ribosome structures have revealed about the mechanism of translation

(2009) T. Martin Schmeing et al.   NATURE

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Reconstruction algorithm for single-particle diffraction imaging experiments

(2009) Ne-Te Duane Loh et al.   PHYSICAL REVIEW E

Protein-protein crystal-packing contacts

(2009) Oliviero Carugo et al.   PROTEIN SCIENCE

Determination of Protein Structures—A Series of Fortunate Events

(2008) Maksymilian Chruszcz et al.   BIOPHYSICAL JOURNAL

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Simulations of Solute Transport in Xylose Isomerase Crystals

(2008) Kourosh Malek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations for Water and Ions in Protein Crystals

(2008) Zhongqiao Hu et al.   LANGMUIR

A structural understanding of the dynamic ribosome machine

(2008) Thomas A. Steitz   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

(2008) Maya Topf et al.   STRUCTURE

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE

Normal-Mode Flexible Fitting of High-Resolution Structure of Biological Molecules toward One-Dimensional Low-Resolution Data

(2007) Christian Gorba et al.   BIOPHYSICAL JOURNAL