Cargando…

DeepRefiner: high-accuracy protein structure refinement by deep network calibration

The DeepRefiner webserver, freely available at http://watson.cse.eng.auburn.edu/DeepRefiner/, is an interactive and fully configurable online system for high-accuracy protein structure refinement. Fuelled by deep learning, DeepRefiner offers the ability to leverage cutting-edge deep neural network a...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shuvo, Md Hossain, Gulfam, Muhammad, Bhattacharya, Debswapna
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Web Server Issue
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262753/ https://www.ncbi.nlm.nih.gov/pubmed/33999209 http://dx.doi.org/10.1093/nar/gkab361

Ejemplares similares

3Drefine: an interactive web server for efficient protein structure refinement
por: Bhattacharya, Debswapna, et al.
Publicado: (2016)

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure
por: Lee, Gyu Rie, et al.
Publicado: (2019)

Galaxy7TM: flexible GPCR–ligand docking by structure refinement
por: Lee, Gyu Rie, et al.
Publicado: (2016)

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics
por: Labbé, Céline M., et al.
Publicado: (2017)

ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates
por: Shuid, Ahmad N., et al.
Publicado: (2017)

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking
por: Wu, Qi, et al.
Publicado: (2018)

ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
por: Adiyaman, Recep, et al.
Publicado: (2021)

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning
por: Xie, Yubin, et al.
Publicado: (2018)

MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization
por: Wang, Duolin, et al.
Publicado: (2020)

deepTools2: a next generation web server for deep-sequencing data analysis
por: Ramírez, Fidel, et al.
Publicado: (2016)

DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations
por: Song, Qianqian, et al.
Publicado: (2023)

NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning
por: Høie, Magnus Haraldson, et al.
Publicado: (2022)

PRECOGx: exploring GPCR signaling mechanisms with deep protein representations
por: Matic, Marin, et al.
Publicado: (2022)

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
por: Kulmanov, Maxat, et al.
Publicado: (2021)

DDMut: predicting effects of mutations on protein stability using deep learning
por: Zhou, Yunzhuo, et al.
Publicado: (2023)

PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants
por: Zhao, Hu, et al.
Publicado: (2021)

DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction
por: Zhou, Xiaogen, et al.
Publicado: (2022)

Deep phenotyping: symptom annotation made simple with SAMS
por: Steinhaus, Robin, et al.
Publicado: (2022)

DeepNeo: a webserver for predicting immunogenic neoantigens
por: Kim, Jeong Yeon, et al.
Publicado: (2023)

MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels
por: Jiang, Yuexu, et al.
Publicado: (2023)

DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner
por: Pei, Guangsheng, et al.
Publicado: (2021)

ComplexContact: a web server for inter-protein contact prediction using deep learning
por: Zeng, Hong, et al.
Publicado: (2018)

DeepLoc 2.0: multi-label subcellular localization prediction using protein language models
por: Thumuluri, Vineet, et al.
Publicado: (2022)

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation
por: Zheng, Wei, et al.
Publicado: (2022)

NAPS: Network Analysis of Protein Structures
por: Chakrabarty, Broto, et al.
Publicado: (2016)

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning
por: Rodrigues, Carlos H M, et al.
Publicado: (2022)

DLEB: a web application for building deep learning models in biological research
por: Wy, Suyeon, et al.
Publicado: (2022)

RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction
por: Wang, Yunxia, et al.
Publicado: (2023)

TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning
por: Yin, Rui, et al.
Publicado: (2023)

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets
por: Albrecht, Felipe, et al.
Publicado: (2016)

G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers
por: Zeng, Shuai, et al.
Publicado: (2021)

QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks
por: Shuvo, Md Hossain, et al.
Publicado: (2020)

ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
por: Aydınkal, Rasim Murat, et al.
Publicado: (2019)

RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles
por: Clementel, Damiano, et al.
Publicado: (2022)

NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation
por: Sakthivel, Seethalakshmi, et al.
Publicado: (2015)

ProteinTools: a toolkit to analyze protein structures
por: Ferruz, Noelia, et al.
Publicado: (2021)

BCSearch: fast structural fragment mining over large collections of protein structures
por: Guyon, Frédéric, et al.
Publicado: (2015)

mTM-align: a server for fast protein structure database search and multiple protein structure alignment
por: Dong, Runze, et al.
Publicado: (2018)

PredictProtein - Predicting Protein Structure and Function for 29 Years
por: Bernhofer, Michael, et al.
Publicado: (2021)

ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes
por: Hua, Zhi-Gang, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_r0omv4aui0gs8fr7ppg8hfu8io