Cargando…

Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. Howe...

Descripción completa

Detalles Bibliográficos
Autores principales:	Roche, Daniel Barry, Brackenridge, Danielle Allison, McGuffin, Liam James
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2015
Materias:	Review
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691145/ https://www.ncbi.nlm.nih.gov/pubmed/26694353 http://dx.doi.org/10.3390/ijms161226202

Ejemplares similares

FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions
por: Roche, Daniel B., et al.
Publicado: (2012)

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

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
por: Roche, Daniel B, et al.
Publicado: (2011)

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
por: Roche, Daniel B., et al.
Publicado: (2011)

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures
por: Nealon, John Oliver, et al.
Publicado: (2017)

Methods for the Refinement of Protein Structure 3D Models
por: Adiyaman, Recep, et al.
Publicado: (2019)

IntFOLD: an integrated web resource for high performance protein structure and function prediction
por: McGuffin, Liam J, et al.
Publicado: (2019)

The ModFOLD4 server for the quality assessment of 3D protein models
por: McGuffin, Liam J., et al.
Publicado: (2013)

Benchmarking consensus model quality assessment for protein fold recognition
por: McGuffin, Liam J
Publicado: (2007)

Are the integrin binding motifs within SARS CoV-2 spike protein and MHC class II alleles playing the key role in COVID-19?
por: Gerencer, Marijan, et al.
Publicado: (2023)

Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies
por: Atkins, Jennifer D., et al.
Publicado: (2015)

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

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

PINOT: an intuitive resource for integrating protein-protein interactions
por: Tomkins, James E., et al.
Publicado: (2020)

Exploring the computational methods for protein-ligand binding site prediction
por: Zhao, Jingtian, et al.
Publicado: (2020)

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences
por: McGuffin, Liam J., et al.
Publicado: (2015)

ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models
por: Maghrabi, Ali H. A., et al.
Publicado: (2017)

Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process
por: Adiyaman, Recep, et al.
Publicado: (2023)

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

Comparison of Different Ranking Methods in Protein-Ligand Binding Site Prediction
por: Gao, Jun, et al.
Publicado: (2012)

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites
por: Xie, Zhong-Ru, et al.
Publicado: (2013)

Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers
por: McGuffin, Liam J, et al.
Publicado: (2023)

Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions
por: Manzi, Lucio, et al.
Publicado: (2016)

Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation
por: Tsujikawa, Hiroto, et al.
Publicado: (2016)

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

Protein structure prediction servers at University College London
por: Bryson, Kevin, et al.
Publicado: (2005)

Ligand-binding site prediction of proteins based on known fragment–fragment interactions
por: Kasahara, Kota, et al.
Publicado: (2010)

Prediction of Protein Ion–Ligand Binding Sites with ELECTRA
por: Essien, Clement, et al.
Publicado: (2023)

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites
por: Shoemaker, Benjamin A., et al.
Publicado: (2010)

Sequence variation in ligand binding sites in proteins
por: Magliery, Thomas J, et al.
Publicado: (2005)

3DLigandSite: structure-based prediction of protein–ligand binding sites
por: McGreig, Jake E, et al.
Publicado: (2022)

ModFOLD8: accurate global and local quality estimates for 3D protein models
por: McGuffin, Liam J, et al.
Publicado: (2021)

A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
por: Dai, Tianli, et al.
Publicado: (2011)

An Accurate Method for Prediction of Protein-Ligand Binding Site on Protein Surface Using SVM and Statistical Depth Function
por: Wang, Kui, et al.
Publicado: (2013)

Cloud Computing for Protein-Ligand Binding Site Comparison
por: Hung, Che-Lun, et al.
Publicado: (2013)

Paramagnetic Ligand Tagging To Identify Protein Binding Sites
por: Brath, Ulrika, et al.
Publicado: (2015)

Specificity of broad protein interaction surfaces for proteins with multiple binding partners
por: Uchikoga, Nobuyuki, et al.
Publicado: (2016)

Predicting small ligand binding sites in proteins using backbone structure
por: Bordner, Andrew J.
Publicado: (2008)

Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
por: Komiyama, Yusuke, et al.
Publicado: (2016)

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
por: Ammar, Ammar, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_0969tup5jcrb3nmcmgf9qmpbnk