Cargando…

Protein structure predictions by enhanced conformational sampling methods

In this Special Festschrift Issue for the celebration of Professor Nobuhiro Gō’s 80th birthday, we review enhanced conformational sampling methods for protein structure predictions. We present several generalized-ensemble algorithms such as multicanonical algorithm, replica-exchange method, etc. and...

Descripción completa

Detalles Bibliográficos
Autor principal:	Okamoto, Yuko
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	The Biophysical Society of Japan (BSJ) 2019
Materias:	Review Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976031/ https://www.ncbi.nlm.nih.gov/pubmed/31984190 http://dx.doi.org/10.2142/biophysico.16.0_344

Ejemplares similares

Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods
por: Denarie, Laurent, et al.
Publicado: (2018)

Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins
por: Markwick, Phineus R. L., et al.
Publicado: (2010)

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes
por: Higo, Junichi, et al.
Publicado: (2012)

Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview
por: Li, Yaohang
Publicado: (2013)

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation
por: Iida, Shinji, et al.
Publicado: (2016)

Sampling of the conformational landscape of small proteins with Monte Carlo methods
por: Heilmann, Nana, et al.
Publicado: (2020)

Sampling Realistic Protein Conformations Using Local Structural Bias
por: Hamelryck, Thomas, et al.
Publicado: (2006)

Pathfinder: Protein folding pathway prediction based on conformational sampling
por: Huang, Zhaohong, et al.
Publicado: (2023)

Enhancing Conformational Sampling for Intrinsically Disordered and Ordered Proteins by Variational Autoencoder
por: Zhu, Jun-Jie, et al.
Publicado: (2023)

Computational methods for exploring protein conformations
por: Allison, Jane R.
Publicado: (2020)

Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction
por: Zaman, Ahmed Bin, et al.
Publicado: (2019)

Addressing the Role of Conformational Diversity in Protein Structure Prediction
por: Palopoli, Nicolas, et al.
Publicado: (2016)

A Structure-free Method for Quantifying Conformational Flexibility in proteins
por: Burger, Virginia M., et al.
Publicado: (2016)

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
por: Li, Jilong, et al.
Publicado: (2015)

Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling
por: Dokainish, Hisham M., et al.
Publicado: (2020)

Sampling the conformation of protein surface residues for flexible protein docking
por: Francis-Lyon, Patricia, et al.
Publicado: (2010)

Predicting Inactive Conformations of Protein Kinases Using Active Structures: Conformational Selection of Type-II Inhibitors
por: Xu, Min, et al.
Publicado: (2011)

Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock
por: Torchala, Mieczyslaw, et al.
Publicado: (2019)

A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling
por: Wang, Zhiyong, et al.
Publicado: (2011)

Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems
por: Okamoto, Kenji, et al.
Publicado: (2017)

Insights into the Structural Conformations of the Tau Protein in Different Aggregation Status
por: Pinzi, Luca, et al.
Publicado: (2023)

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems
por: Lazim, Raudah, et al.
Publicado: (2020)

DESP: Deep Enhanced Sampling of Proteins’ Conformation Spaces Using AI-Inspired Biasing Forces
por: Salawu, Emmanuel Oluwatobi
Publicado: (2021)

Structural coordinates: A novel approach to predict protein backbone conformation
por: Milchevskaya, Vladislava, et al.
Publicado: (2021)

Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins
por: Beveridge, Rebecca, et al.
Publicado: (2021)

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
por: Kaynak, Burak T., et al.
Publicado: (2022)

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules
por: Schlick, Tamar
Publicado: (2009)

Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling
por: Rakotoharisoa, Rojo V., et al.
Publicado: (2023)

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
por: Devaurs, Didier, et al.
Publicado: (2017)

Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data
por: Devaurs, Didier, et al.
Publicado: (2018)

Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology
por: Grasso, Daniela, et al.
Publicado: (2023)

Deep learning methods in protein structure prediction
por: Torrisi, Mirko, et al.
Publicado: (2020)

Protein–protein interaction prediction methods: from docking-based to AI-based approaches
por: Tsuchiya, Yuko, et al.
Publicado: (2022)

Pyrene: A Probe to Study Protein Conformation and Conformational Changes
por: Bains, Gursharan, et al.
Publicado: (2011)

Conformational Change of Amyloid-β 40 in Association with Binding to GM1-Glycan Cluster
por: Tachi, Yuhei, et al.
Publicado: (2019)

Knowledge-based prediction of protein backbone conformation using a structural alphabet
por: Vetrivel, Iyanar, et al.
Publicado: (2017)

Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures
por: Al-Masri, Carmen, et al.
Publicado: (2023)

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
por: Gil-Ley, Alejandro, et al.
Publicado: (2015)

Machine learning/molecular dynamic protein structure prediction approach to investigate the protein conformational ensemble
por: Audagnotto, Martina, et al.
Publicado: (2022)

Using Local States To Drive the Sampling of Global Conformations in Proteins
por: Pandini, Alessandro, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_g22m1kmu8f2q97s2frj7audml1