Cargando…

Adaptive simulations, towards interactive protein-ligand modeling

Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few years hardware and software advances have significantly revamped the use of mol...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lecina, Daniel, Gilabert, Joan F., Guallar, Victor
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2017
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559483/ https://www.ncbi.nlm.nih.gov/pubmed/28814780 http://dx.doi.org/10.1038/s41598-017-08445-5

Ejemplares similares

Towards the simulation of large scale protein–ligand interactions on NISQ-era quantum computers
por: Malone, Fionn D., et al.
Publicado: (2022)

The unravelling of the complex pattern of tyrosinase inhibition
por: Deri, Batel, et al.
Publicado: (2016)

Mutations Suppressing the Lack of Prepilin Peptidase Provide Insights Into the Maturation of the Major Pilin Protein in Cyanobacteria
por: Linhartová, Markéta, et al.
Publicado: (2021)

Atomistic simulations shed new light on the activation mechanisms of RORγ and classify it as Type III nuclear hormone receptor regarding ligand-binding paths
por: Saen-Oon, Suwipa, et al.
Publicado: (2019)

Estimation of the protein–ligand interaction energy for model building and validation
por: Beshnova, Daria A., et al.
Publicado: (2017)

Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation
por: Fukunishi, Yoshifumi, et al.
Publicado: (2012)

Molecular simulations of SSTR2 dynamics and interaction with ligands
por: Gervasoni, Silvia, et al.
Publicado: (2023)

Structure and Ligands Interactions of Citrus Tryptophan Decarboxylase by Molecular Modeling and Docking Simulations
por: Facchiano, Angelo, et al.
Publicado: (2019)

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands
por: Koschek, Katharina, et al.
Publicado: (2015)

Small molecule interactions with the SARS-CoV-2 main protease: In silico all-atom microsecond MD simulations, PELE Monte Carlo simulations, and determination of in vitro activity inhibition
por: Liang, Julia, et al.
Publicado: (2022)

Protein Ligands to Hur Modulate Its Interaction with Target Mrnas in Vivo
por: Brennan, Christopher M., et al.
Publicado: (2000)

Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose
por: Díaz, Lucía, et al.
Publicado: (2020)

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods
por: Du, Xing, et al.
Publicado: (2016)

A quantum chemical interaction energy dataset for accurately modeling protein-ligand interactions
por: Spronk, Steven A., et al.
Publicado: (2023)

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
por: Gygli, Gudrun, et al.
Publicado: (2017)

Preparative Scale Production of Recombinant Human Transthyretin for Biophysical Studies of Protein-Ligand and Protein-Protein Interactions
por: Cotrina, Ellen Y., et al.
Publicado: (2020)

Towards Adaptive Grids for Atmospheric Boundary-Layer Simulations
por: van Hooft, J. Antoon, et al.
Publicado: (2018)

The protein flexibility in receptor-ligand docking simulations
por: Tristram, Frank
Publicado: (2010)

Exploiting Ligand-Protein Conjugates to Monitor Ligand-Receptor Interactions
por: Haruki, Hirohito, et al.
Publicado: (2012)

A flexible-hydrogen interaction model for protein-ligand docking
por: Henzler, Angela M, et al.
Publicado: (2012)

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge
por: Giri, Nabin, et al.
Publicado: (2023)

Colloidal-ALD-Grown Metal Oxide Shells Enable the Synthesis of Photoactive Ligand/Nanocrystal Composite Materials
por: Green, Philippe B., et al.
Publicado: (2023)

Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures
por: Greenside, Peyton, et al.
Publicado: (2018)

Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites
por: Marsh, Lorraine
Publicado: (2015)

Simulating protein–ligand binding with neural network potentials
por: Lahey, Shae-Lynn J., et al.
Publicado: (2020)

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model
por: Benayad, Zakarya, et al.
Publicado: (2020)

Predicting target-ligand interactions using protein ligand-binding site and ligand substructures
por: Wang, Caihua, et al.
Publicado: (2015)

PLIC: protein–ligand interaction clusters
por: Anand, Praveen, et al.
Publicado: (2014)

Characterization of protein–ligand interactions by SABRE
por: Mandal, Ratnamala, et al.
Publicado: (2021)

Structural Insights into σ(1) Receptor Interactions with Opioid Ligands by Molecular Dynamics Simulations
por: Kurciński, Mateusz, et al.
Publicado: (2018)

Predicting Antibody Neutralization Efficacy in Hypermutated Epitopes Using Monte Carlo Simulations
por: Amengual-Rigo, Pep, et al.
Publicado: (2020)

Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein
por: Fu, Yi, et al.
Publicado: (2018)

Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol
por: Tavares, Diogo, et al.
Publicado: (2021)

The FunFOLD2 server for the prediction of protein–ligand interactions
por: Roche, Daniel B., et al.
Publicado: (2013)

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
por: Plattner, Nuria, et al.
Publicado: (2015)

Prediction of Protein–ligand Interaction Based on Sequence Similarity and Ligand Structural Features
por: Karasev, Dmitry, et al.
Publicado: (2020)

Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions
por: Koehl, Antoine, et al.
Publicado: (2022)

HEK293 cell culture media study: increasing cell density for different bioprocess applications
por: Liste-Calleja, Leticia, et al.
Publicado: (2013)

Mass spectrometric analysis of protein–ligand interactions
por: Ishii, Kentaro, et al.
Publicado: (2016)

Toward Dynamically Adaptive Simulation: Multimodal Classification of User Expertise Using Wearable Devices
por: Ross, Kyle, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_b2urdq4uf6vha3h440j7g93o0q