Cargando…

Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification

BACKGROUND: The maintenance of protein structural stability requires the cooperativity among spatially neighboring residues. Previous studies have shown that conserved residues tend to occur clustered together within enzyme active sites and protein-protein/DNA interfaces. It is possible that conserv...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yang, Zhen, Deng, Xueqing, Liu, Yang, Gong, Weikang, Li, Chunhua
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2020
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7027071/ https://www.ncbi.nlm.nih.gov/pubmed/32066366 http://dx.doi.org/10.1186/s12859-020-3398-9

Ejemplares similares

Conserved residue clusters at protein-protein interfaces and their use in binding site identification
por: Guharoy, Mainak, et al.
Publicado: (2010)

Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites
por: Kang, Keunsoo, et al.
Publicado: (2009)

Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
por: Dong, Qiwen, et al.
Publicado: (2007)

Prediction of protein-protein binding site by using core interface residue and support vector machine
por: Li, Nan, et al.
Publicado: (2008)

Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
por: Ahmad, Shandar, et al.
Publicado: (2008)

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
por: Berman, Benjamin P, et al.
Publicado: (2004)

CCRXP: exploring clusters of conserved residues in protein structures
por: Ahmad, Shandar, et al.
Publicado: (2010)

Evolutionary conservation of DNA-contact residues in DNA-binding domains
por: Chang, Yao-Lin, et al.
Publicado: (2008)

Docking-based identification of small-molecule binding sites at protein-protein interfaces
por: Rosell, Mireia, et al.
Publicado: (2020)

Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters
por: Dey, Sucharita, et al.
Publicado: (2012)

Being a binding site: Characterizing residue composition of binding sites on proteins
por: Iván, Gábor, et al.
Publicado: (2007)

Discovery of novel helix binding sites at protein-protein interfaces
por: Yang, Wei, et al.
Publicado: (2019)

Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface
por: Söderberg, Christopher A. G., et al.
Publicado: (2018)

Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16
por: Kozielski, Frank, et al.
Publicado: (2021)

Identification of hot spot residues at protein-protein interface
por: Li, Lei, et al.
Publicado: (2006)

CONREAL web server: identification and visualization of conserved transcription factor binding sites
por: Berezikov, Eugene, et al.
Publicado: (2005)

Conserved Calcium-Binding Residues at the Ca-I Site Involved in Fructooligosaccharide Synthesis by Lactobacillus reuteri 121 Inulosucrase
por: Charoenwongpaiboon, Thanapon, et al.
Publicado: (2020)

Identification of critical residues in loop E in the 5-HT(3AS)R binding site
por: Venkataraman, Padmavati, et al.
Publicado: (2002)

Rapid Identification of Secondary Structure and Binding Site Residues in an Intrinsically Disordered Protein Segment
por: Chandra, Soumyanetra, et al.
Publicado: (2021)

Regulatory patterns analysis of transcription factor binding site clustered regions and identification of key genes in endometrial cancer
por: Tang, Xiaohan, et al.
Publicado: (2022)

SiteEngines: recognition and comparison of binding sites and protein–protein interfaces
por: Shulman-Peleg, Alexandra, et al.
Publicado: (2005)

Combining specificity determining and conserved residues improves functional site prediction
por: Kalinina, Olga V, et al.
Publicado: (2009)

Roles of conserved active site residues in the IscS cysteine desulfurase reaction
por: Pang, Yilin, et al.
Publicado: (2023)

Structure-function analyses of metal-binding sites of HypA reveal residues important for hydrogenase maturation in Helicobacter pylori
por: Blum, Faith C., et al.
Publicado: (2017)

POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster
por: Farley, Brian M., et al.
Publicado: (2012)

Interaction between residues in the Mg(2+)-binding site regulates BK channel activation
por: Yang, Junqiu, et al.
Publicado: (2013)

Predicting RNA-binding residues from evolutionary information and sequence conservation
por: Huang, Yu-Feng, et al.
Publicado: (2010)

Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier
por: Duncan, Anna L., et al.
Publicado: (2018)

Identification and mutational analyses of phosphorylation sites of the calcineurin-binding protein CbpA and the identification of domains required for calcineurin binding in Aspergillus fumigatus
por: Juvvadi, Praveen R., et al.
Publicado: (2015)

Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors
por: Ribeiro, Cristina, et al.
Publicado: (2010)

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
por: Hestand, Matthew S, et al.
Publicado: (2008)

Bone remodeling at microscrew interface near extraction site in the beagle dog mandible-histologic and immunohistochemical analyses
por: WEI, Guangxi, et al.
Publicado: (2013)

Antigenic conservation and immunogenicity of the HIV coreceptor binding site
por: Decker, Julie M., et al.
Publicado: (2005)

Contribution of ribosomal residues to P-site tRNA binding
por: Shoji, Shinichiro, et al.
Publicado: (2009)

Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis
por: Khushi, Matloob, et al.
Publicado: (2014)

Conservation of Carbohydrate Binding Interfaces — Evidence of Human HBGA Selection in Norovirus Evolution
por: Tan, Ming, et al.
Publicado: (2009)

Amino acid residue doublet propensity in the protein–RNA interface and its application to RNA interface prediction
por: Kim, Oanh T. P., et al.
Publicado: (2006)

Initial Coupling of Binding to Gating Mediated by Conserved Residues in the Muscle Nicotinic Receptor
por: Mukhtasimova, Nuriya, et al.
Publicado: (2005)

Identifying RNA-binding residues based on evolutionary conserved structural and energetic features
por: Chen, Yao Chi, et al.
Publicado: (2014)

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
por: Totrov, Maxim
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_2hbb355jlmeqjtlvpumel26jqp