Cargando…

pyDockSAXS: protein–protein complex structure by SAXS and computational docking

Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structur...

Descripción completa

Detalles Bibliográficos
Autores principales:	Jiménez-García, Brian, Pons, Carles, Svergun, Dmitri I., Bernadó, Pau, Fernández-Recio, Juan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2015
Materias:	Web Server issue
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489248/ https://www.ncbi.nlm.nih.gov/pubmed/25897115 http://dx.doi.org/10.1093/nar/gkv368

Ejemplares similares

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
por: Knight, Christopher J., et al.
Publicado: (2015)

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles
por: Schneidman-Duhovny, Dina, et al.
Publicado: (2016)

HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
por: Weng, Gaoqi, et al.
Publicado: (2019)

CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting
por: Liu, Yang, et al.
Publicado: (2022)

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information
por: Yu, Jinchao, et al.
Publicado: (2016)

LZerD webserver for pairwise and multiple protein–protein docking
por: Christoffer, Charles, et al.
Publicado: (2021)

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
por: Lee, Hasup, et al.
Publicado: (2015)

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
por: Kurcinski, Mateusz, et al.
Publicado: (2015)

NPDock: a web server for protein–nucleic acid docking
por: Tuszynska, Irina, et al.
Publicado: (2015)

Identification and visualization of protein binding regions with the ArDock server
por: Reille, Sébastien, et al.
Publicado: (2018)

InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs
por: Quignot, Chloé, et al.
Publicado: (2018)

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions
por: Jiménez-García, Brian, et al.
Publicado: (2023)

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy
por: Yan, Yumeng, et al.
Publicado: (2017)

The pepATTRACT web server for blind, large-scale peptide–protein docking
por: de Vries, Sjoerd J., et al.
Publicado: (2017)

GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
por: Park, Taeyong, et al.
Publicado: (2021)

HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm
por: Zhou, Pei, et al.
Publicado: (2018)

HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry
por: Yan, Yumeng, et al.
Publicado: (2018)

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

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

InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps
por: Quignot, Chloé, et al.
Publicado: (2021)

systemsDock: a web server for network pharmacology-based prediction and analysis
por: Hsin, Kun-Yi, et al.
Publicado: (2016)

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
por: He, Jiahua, et al.
Publicado: (2019)

nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands
por: Liu, Kai, et al.
Publicado: (2023)

CASTp 3.0: computed atlas of surface topography of proteins
por: Tian, Wei, et al.
Publicado: (2018)

pyDockDNA: A new web server for energy-based protein-DNA docking and scoring
por: Rodríguez-Lumbreras, Luis Angel, et al.
Publicado: (2022)

PepComposer: computational design of peptides binding to a given protein surface
por: Obarska-Kosinska, Agnieszka, et al.
Publicado: (2016)

Kinact: a computational approach for predicting activating missense mutations in protein kinases
por: Rodrigues, Carlos HM, et al.
Publicado: (2018)

A PanorOmic view of personal cancer genomes
por: Mateo, Lidia, et al.
Publicado: (2017)

SAX2
por: Brownell, David
Publicado: (2002)

ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling
por: Cheng, Yiming, et al.
Publicado: (2015)

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
por: Zhang, Chengxin, et al.
Publicado: (2017)

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

Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions
por: Roy, Ankit A, et al.
Publicado: (2019)

The Proteins API: accessing key integrated protein and genome information
por: Nightingale, Andrew, et al.
Publicado: (2017)

ProteinsPlus: interactive analysis of protein–ligand binding interfaces
por: Schöning-Stierand, Katrin, et al.
Publicado: (2020)

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

Peptiderive server: derive peptide inhibitors from protein–protein interactions
por: Sedan, Yuval, et al.
Publicado: (2016)

MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions
por: Li, Minghui, et al.
Publicado: (2016)

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions
por: Rodrigues, Carlos H M, et al.
Publicado: (2019)

VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes
por: Olechnovič, Kliment, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_8uiirqp3mpsfv16iguvrfe3rv6