Cargando…

Multi-shelled ECIF: improved extended connectivity interaction features for accurate binding affinity prediction

MOTIVATION: Extended connectivity interaction features (ECIF) is a method developed to predict protein–ligand binding affinity, allowing for detailed atomic representation. It performed very well in terms of Comparative Assessment of Scoring Functions 2016 (CASF-2016) scoring power. However, ECIF ha...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shiota, Koji, Akutsu, Tatsuya
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Original Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10625475/ https://www.ncbi.nlm.nih.gov/pubmed/37928345 http://dx.doi.org/10.1093/bioadv/vbad155

Ejemplares similares

A simple spatial extension to the extended connectivity interaction features for binding affinity prediction
por: Orhobor, Oghenejokpeme I., et al.
Publicado: (2022)

Women Versus Men with Chronic Atrial Fibrillation: Insights from the Standard Versus Atrial Fibrillation spEcific managemenT studY (SAFETY)
por: Ball, Jocasta, et al.
Publicado: (2013)

Accurate and sensitive quantification of protein-DNA binding affinity
por: Rastogi, Chaitanya, et al.
Publicado: (2018)

Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions
por: Wójcikowski, Maciej, et al.
Publicado: (2019)

SophosQM: Accurate Binding Affinity Prediction in Compound Optimization
por: Guareschi, Riccardo, et al.
Publicado: (2023)

DataDTA: a multi-feature and dual-interaction aggregation framework for drug–target binding affinity prediction
por: Zhu, Yan, et al.
Publicado: (2023)

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation
por: Aldeghi, Matteo, et al.
Publicado: (2018)

Learned features of antibody-antigen binding affinity
por: Miller, Nathaniel L., et al.
Publicado: (2023)

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction
por: You, Ronghui, et al.
Publicado: (2022)

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
por: Kato, Yuki, et al.
Publicado: (2010)

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE
por: Riley, Todd R, et al.
Publicado: (2015)

Accurate phosphoregulation of kinetochore–microtubule affinity requires unconstrained molecular interactions
por: Zaytsev, Anatoly V., et al.
Publicado: (2014)

DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
por: Qu, Wei, et al.
Publicado: (2023)

Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features
por: Bao, Yu, et al.
Publicado: (2018)

Prediction of Protein-Protein Interaction Strength Using Domain Features with Supervised Regression
por: Kamada, Mayumi, et al.
Publicado: (2014)

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
por: Schmidt, Florian, et al.
Publicado: (2017)

FATHMM-XF: accurate prediction of pathogenic point mutations via extended features
por: Rogers, Mark F, et al.
Publicado: (2018)

On the binding affinity of macromolecular interactions: daring to ask why proteins interact
por: Kastritis, Panagiotis L., et al.
Publicado: (2013)

Methods for Improving Aptamer Binding Affinity
por: Hasegawa, Hijiri, et al.
Publicado: (2016)

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming
por: Kato, Yuki, et al.
Publicado: (2012)

Prediction of Heterodimeric Protein Complexes from Weighted Protein-Protein Interaction Networks Using Novel Features and Kernel Functions
por: Ruan, Peiying, et al.
Publicado: (2013)

MSGNN-DTA: Multi-Scale Topological Feature Fusion Based on Graph Neural Networks for Drug–Target Binding Affinity Prediction
por: Wang, Shudong, et al.
Publicado: (2023)

Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation
por: Goel, Himanshu, et al.
Publicado: (2021)

mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity
por: Nguyen, Thanh Binh, et al.
Publicado: (2021)

Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation
por: Mohseni Behbahani, Yasser, et al.
Publicado: (2023)

Extended affine Lie algebras and their root systems
por: Allison, Bruce N, et al.
Publicado: (1997)

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
por: Sato, Kengo, et al.
Publicado: (2011)

Extended photoresponse and multi-band luminescence of ZnO/ZnSe core/shell nanorods
por: Yang, Qin, et al.
Publicado: (2014)

Accurate Determination of the Oxidative Phosphorylation Affinity for ADP in Isolated Mitochondria
por: Gouspillou, Gilles, et al.
Publicado: (2011)

Instrument-Free Protein Microarray Fabrication for Accurate Affinity Measurements
por: Celebi, Iris, et al.
Publicado: (2020)

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
por: Ballester, Pedro J., et al.
Publicado: (2014)

AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks
por: Kwon, Yongbeom, et al.
Publicado: (2020)

MRBLE-pep Measurements Reveal Accurate Binding Affinities for B56, a PP2A Regulatory Subunit
por: Hein, Jamin B., et al.
Publicado: (2021)

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features
por: Wang, Liangjiang, et al.
Publicado: (2010)

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
por: Manke, Thomas, et al.
Publicado: (2008)

Structure-based protein–ligand interaction fingerprints for binding affinity prediction
por: Wang, Debby D., et al.
Publicado: (2021)

A shell dataset, for shell features extraction and recognition
por: Zhang, Qi, et al.
Publicado: (2019)

From closed-shell edge-extended kekulenes to open-shell carbonylated cycloarene diradicaloid
por: Chang, Dongdong, et al.
Publicado: (2023)

Extending the Affinity Range of Weak Affinity Chromatography for the Identification of Weak Ligands Targeting Membrane Proteins
por: Deloche, Adrien, et al.
Publicado: (2023)

An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
por: Tiwari, Garima, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_71khadjq163kc8n6m3g7vcvqfq