4.2 Article

Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation

Remi Vuillemot et al.

Summary: This article presents a new method for extracting atomic-resolution landscapes of continuous conformational variability of biomolecular complexes from cryo-EM single particle images. The method, called MDSPACE, uses a 3D-to-2D flexible fitting method based on molecular dynamics simulation and is embedded in an iterative conformational-landscape refinement scheme. The article describes the MDSPACE approach and demonstrates its performance using synthetic and experimental datasets.

JOURNAL OF MOLECULAR BIOLOGY (2023)

Article Multidisciplinary Sciences

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

D. Herreros et al.

Summary: The advancements in Cryo-EM Single Particle Analysis play a vital role in understanding the relationship between macromolecular structure and function in biological processes. Traditional approaches have limitations in fully characterizing the conformational landscape due to the small number of accurately reconstructed states. To overcome this, we propose an extension of the Zernike3D method that can extract continuous flexibility information directly from particle datasets. Additionally, the introduced ZART reconstruction algorithm minimizes blurring induced by molecular motions.

NATURE COMMUNICATIONS (2023)

Article Biochemistry & Molecular Biology

ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis

D. Herreros et al.

Summary: The main purpose of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule. ZART is a new Algebraic Reconstruction Technique that can include continuous flexibility information to improve resolution and reduce motion blurring.

JOURNAL OF MOLECULAR BIOLOGY (2023)

Article Biochemistry & Molecular Biology

TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow

Mohamad Harastani et al.

Summary: This paper introduces a method called TomoFlow, which utilizes three-dimensional dense optical flow (OF) to analyze the continuous conformational variability of macromolecules in cryogenic electron tomography (cryo-ET). The method can generate animations of macromolecular motion and obtain averages of subtomograms by grouping similar conformations.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Article Biochemistry & Molecular Biology

NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements

Remi Vuillemot et al.

Summary: This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD), to obtain atomic models of cryo-EM maps more efficiently and accurately.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Article Biochemistry & Molecular Biology

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation

J. Jimenez de la Morena et al.

Summary: This article introduces the extension of Scipion framework, called ScipionTomo, aiming to simplify image processing and analysis in cryogenic electron tomography. Developed by a collaborative multidisciplinary team, it combines the knowledge of Scipion developers with functionalities requested by beta testers and integrates third-party software packages.

JOURNAL OF STRUCTURAL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Dali server: structural unification of protein families

Liisa Holm

Summary: Protein structure is crucial for understanding biological function, and recent advancements in deep learning have revolutionized the field of structural bioinformatics. The Dali server for protein structure comparison has been upgraded to allow searching for foldomes of key organisms in the AlphaFold Database and to provide annotated structural alignments with protein families.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data

Mohamad Harastani et al.

Summary: ContinuousFlex is an open-source software package for analyzing continuous conformational variability of macromolecules in cryo-EM and cryo-ET data. It includes various methods and external software, with some methods available in Scipion and a deep learning extension provided. The software is developed to facilitate the use by the community.

JOURNAL OF STRUCTURAL BIOLOGY (2022)

Article Materials Science, Multidisciplinary

3D Flexible Refinement: Structure and Motion of Flexible Proteins from Cryo-EM

Ali Punjani et al.

MICROSCOPY AND MICROANALYSIS (2022)

Article Biochemistry & Molecular Biology

DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images

Ilyes Hamitouche et al.

Summary: Single-particle cryo-electron microscopy (cryo-EM) is a technique for biomolecular structure reconstruction. Understanding different conformations is crucial for molecular mechanisms and drug discovery. The new method DeepHEMNMA combines deep learning to speed up analysis.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Review Biochemistry & Molecular Biology

State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps

Yan Zhang et al.

Summary: The eukaryotic chaperonin TRiC/CCT's structure-encoded allosteric dynamics were investigated using computational methods, revealing that the overall architecture favors cooperative movements and sequential events in different states of the allosteric cycle. Individual subunits exhibit state-dependent behaviors, with specific subunits initiating certain motions in response to ATP binding and apo form states. These state-dependent mechanisms provide insights into TRiC/CCT intra- and inter-ring signal transduction events.

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2021)

Article Biochemistry & Molecular Biology

UCSF ChimeraX: Structure visualization for researchers, educators, and developers

Eric F. Pettersen et al.

Summary: UCSF ChimeraX is a powerful visualization program with enhanced performance and graphics, offering new tools and analysis features, support for various areas like virtual reality, and improved ease of use, along with an app store for researchers to contribute new tools.

PROTEIN SCIENCE (2021)

Article Biochemical Research Methods

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

Ellen D. Zhong et al.

Summary: cryoDRGN is an algorithm that uses the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It can uncover residual heterogeneity in high-resolution datasets and visualize large-scale continuous motions of protein complexes, while also offering interactive tools for dataset visualization and analysis.

NATURE METHODS (2021)

Article Cell Biology

Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding

Dhiraj Mannar et al.

Summary: The newly emerged SARS-CoV-2 variants, Beta and Gamma, exhibit key mutations that enhance spike protein affinity for ACE2 receptor and promote antibody evasion. By engineering spike proteins with these mutations and conducting structural analyses, the effects of different variants were studied in terms of increased ACE2 affinity and antibody evasion.

CELL REPORTS (2021)

Article Biochemical Research Methods

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python

She Zhang et al.

Summary: ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in response to the growing data and needs of the computational biology community. The major developments that led to ProDy 2.0 include improved interfacing with databases, signature dynamics, collective dynamics using cryo-EM density maps, and essential site scanning analysis for identifying sites essential to modulating global dynamics.

BIOINFORMATICS (2021)

Article Chemistry, Multidisciplinary

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

David Herreros et al.

Summary: Advancements in technologies like electron microscopy have greatly advanced structural biology, allowing researchers to explore the conformational changes and dynamic events of macromolecules more effectively. A new automatic algorithm based on a mathematical basis defined over the sphere simplifies the analysis of continuous heterogeneity data and provides the ability to comprehensively compare different structural characteristics.
Article Biochemistry & Molecular Biology

HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes

Mohamad Harastani et al.

Summary: "Cryogenic electron tomography (cryo-ET) allows for structural determination of biomolecules in their native environment, but challenges in data analysis have hindered exploration of its potential in studying dynamics of macromolecular complexes within cells. The HEMNMA-3D method presented here addresses the continuous conformational changes of complexes in cryo electron subtomograms by combining elastic and rigid-body 3D-to-3D iterative alignments. These alignments provide insights into the distribution and dynamics of complexes, visualized in lower dimensional space."

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

Article Biochemical Research Methods

Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM

Muyuan Chen et al.

Summary: e2gmm is a machine learning algorithm that utilizes a deep neural network and Gaussian mixture model to resolve structural heterogeneity within protein complexes, mapping changes in conformation and composition. It offers a more intuitive and flexible representation compared to other current manifold methods.

NATURE METHODS (2021)

Article Biochemistry & Molecular Biology

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Mohamad Harastani et al.

PROTEIN SCIENCE (2020)

Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

Article Multidisciplinary Sciences

Distinct conformational states of SARS-CoV-2 spike protein

Yongfei Cai et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity

She Zhang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Chemistry, Multidisciplinary

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Chigusa Kobayashi et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)

Article Biochemical Research Methods

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Ali Punjani et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

Natalie Sauerwald et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Engineering, Electrical & Electronic

Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation

Slavica Jonic et al.

IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING (2016)

Article Biochemistry & Molecular Biology

Local analysis of strains and rotations for macromolecular electron microscopy maps

C. O. S. Sorzano et al.

JOURNAL OF STRUCTURAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

J. M. de la Rosa-Trevin et al.

JOURNAL OF STRUCTURAL BIOLOGY (2016)

Article Biochemical Research Methods

Cryo electron microscopy to determine the structure of macromolecular complexes

Marta Carroni et al.

METHODS (2016)

Review Multidisciplinary Sciences

Principal component analysis: a review and recent developments

Ian T. Jolliffe et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2016)

Article Biochemical Research Methods

Evol and ProDy for bridging protein sequence evolution and structural dynamics

Ahmet Bakan et al.

BIOINFORMATICS (2014)

Article Chemistry, Multidisciplinary

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Jing Huang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)

Article Biochemistry & Molecular Biology

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

Sjors H. W. Scheres

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Article Biochemical Research Methods

NIH Image to ImageJ: 25 years of image analysis

Caroline A. Schneider et al.

NATURE METHODS (2012)

Article Chemistry, Physical

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

H. Lee Woodcock et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Biochemical Research Methods

Anisotropic network model: systematic evaluation and a new web interface

Eran Eyal et al.

BIOINFORMATICS (2006)

Article Physics, Multidisciplinary

Allostery in a coarse-grained model of protein dynamics

D Ming et al.

PHYSICAL REVIEW LETTERS (2005)

Article Biochemistry & Molecular Biology

Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

J Karanicolas et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Biophysics

Anisotropy of fluctuation dynamics of proteins with an elastic network model

AR Atilgan et al.

BIOPHYSICAL JOURNAL (2001)

Article Chemistry, Physical

Harmonicity in slow protein dynamics

K Hinsen et al.

CHEMICAL PHYSICS (2000)