Cargando…

Searching for tunnels of proteins – comparison of approaches and available software tools

Detalles Bibliográficos
Autores principales:	Jaiswal, Deepti, Vařeková, Radka Svobodová, Ionescu, Crina-Maria, Sehnal, David, Koča, Jaroslav
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2012
Materias:	Poster Presentation
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341237/ http://dx.doi.org/10.1186/1758-2946-4-S1-P60

Ejemplares similares

Consistency of sugar structures and their annotation in the PDB
por: Jaiswal, Deepti, et al.
Publicado: (2014)

SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs
por: Sehnal, David, et al.
Publicado: (2012)

QM quality atomic charges for proteins
por: Geidl, Stanislav, et al.
Publicado: (2014)

QSPR designer – employ your own descriptors in the automated QSAR modeling process
por: Skřehota, Ondřej, et al.
Publicado: (2012)

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank
por: Sehnal, David, et al.
Publicado: (2015)

Empirical charges for chemoinformatics applications
por: Bouchal, Tomáš, et al.
Publicado: (2014)

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes
por: Vařeková, Radka Svobodová, et al.
Publicado: (2014)

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
por: Sehnal, David, et al.
Publicado: (2014)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels
por: Berka, Karel, et al.
Publicado: (2012)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)
por: Pravda, Lukáš, et al.
Publicado: (2018)

Predicting pK(a) values from EEM atomic charges
por: Vařeková, Radka Svobodová, et al.
Publicado: (2013)

MOLE 2.0: advanced approach for analysis of biomacromolecular channels
por: Sehnal, David, et al.
Publicado: (2013)

ChannelsDB: database of biomacromolecular tunnels and pores
por: Pravda, Lukáš, et al.
Publicado: (2018)

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
por: Ionescu, Crina-Maria, et al.
Publicado: (2015)

QSPR designer – a program to design and evaluate QSPR models. Case study on pK(a) prediction
por: Skřehota, O, et al.
Publicado: (2011)

How the methodology of 3D structure preparation influences the quality of QSPR models?
por: Geidl, Stanislav, et al.
Publicado: (2012)

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation
por: Ionescu, Crina-Maria, et al.
Publicado: (2012)

Anatomy of enzyme channels
por: Pravda, Lukáš, et al.
Publicado: (2014)

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges
por: Raček, Tomáš, et al.
Publicado: (2016)

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule
por: Vařeková, Radka Svobodová, et al.
Publicado: (2007)

Software for spatial analysis and visualisation of cluster randomised trials - a review of available tools
por: Jarvis, Christopher, et al.
Publicado: (2015)

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
por: Sehnal, David, et al.
Publicado: (2020)

High-performance macromolecular data delivery and visualization for the web. Corrigendum
por: Sehnal, David, et al.
Publicado: (2021)

High-performance macromolecular data delivery and visualization for the web
por: Sehnal, David, et al.
Publicado: (2020)

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations
por: Chareshneu, Aliaksei, et al.
Publicado: (2023)

High-quality and universal empirical atomic charges for chemoinformatics applications
por: Geidl, Stanislav, et al.
Publicado: (2015)

NAChRDB: A Web Resource of Structure–Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors
por: Chareshneu, Aliaksei, et al.
Publicado: (2021)

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
por: Sehnal, David, et al.
Publicado: (2021)

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges
por: Raček, Tomáš, et al.
Publicado: (2020)

Virtual screening and in silico design of novel inhibitors of bacterial lectins
por: Alán, Jan, et al.
Publicado: (2012)

A flexible software tool for fitting the parameters of neuronal models
por: Friedrich, Péter, et al.
Publicado: (2013)

ValTrendsDB: bringing Protein Data Bank validation information closer to the user
por: Horský, Vladimír, et al.
Publicado: (2019)

A software tool for segmentation of the myocardium in CMR exams using level-set algorithm
por: Nazemoroaya, Azadeh, et al.
Publicado: (2016)

Software tools for implementing simulation studies in adaptive seamless designs: introducing R package ASD
por: Parsons, Nick, et al.
Publicado: (2011)

SysWiz database and software tool providing an insight into mechanism of action of molecules associated with ciliopathies
por: Apic, G
Publicado: (2012)

Comprehensive fluid dynamic quantification in congenital heart disease: introduction of a new software tool
por: Gabbert, Dominik Daniel, et al.
Publicado: (2015)

Nemesis - a molecular modeling package
por: Štěpán, Jakub, et al.
Publicado: (2013)

Resistance of neonatal endotracheal tubes: a comparison of four commercially available types
por: Spaeth, J, et al.
Publicado: (2013)

Development of a new software tool and analysis method to improve determination of G6PD status
por: Kalnoky, Michael, et al.
Publicado: (2014)

Optimized SQE atomic charges for peptides accessible via a web application
por: Schindler, Ondřej, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_5rlaqbnolpuvc5t8acleek6mqd