Cargando…

WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design

In this work, two freely available web-based interactive computational tools that facilitate the analysis and interpretation of protein–ligand interaction data are described. Firstly, WONKA, which assists in uncovering interesting and unusual features (for example residue motions) within ensembles o...

Descripción completa

Detalles Bibliográficos
Autores principales:	Deane, Charlotte M., Wall, Ian D., Green, Darren V. S., Marsden, Brian D., Bradley, Anthony R.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	International Union of Crystallography 2017
Materias:	Research Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349440/ https://www.ncbi.nlm.nih.gov/pubmed/28291763 http://dx.doi.org/10.1107/S2059798316009529

Ejemplares similares

OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data
por: Bradley, Anthony R., et al.
Publicado: (2014)

WONKA: objective novel complex analysis for ensembles of protein–ligand structures
por: Bradley, A. R., et al.
Publicado: (2015)

LIGAND-RECEPTOR INTERACTIONS AND DRUG DESIGN
por: Zhang, Yanling, et al.
Publicado: (2015)

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites
por: Pearce, Nicholas M., et al.
Publicado: (2017)

Deep generative design with 3D pharmacophoric constraints
por: Imrie, Fergus, et al.
Publicado: (2021)

Deep Generative Models for 3D Linker Design
por: Imrie, Fergus, et al.
Publicado: (2020)

Identification of selective protein–protein interaction inhibitors using efficient in silico peptide-directed ligand design
por: Beekman, Andrew M., et al.
Publicado: (2019)

Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design
por: Kumar, Akhil, et al.
Publicado: (2018)

In silico peptide-directed ligand design complements experimental peptide-directed binding for protein–protein interaction modulator discovery
por: Howell, Lesley Ann, et al.
Publicado: (2020)

Editorial: Chemoinformatics Approaches to Structure- and Ligand-Based Drug Design
por: Ferreira, Leonardo L. G., et al.
Publicado: (2018)

Structural Characterization of Mycobacterium abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications for Fragment-Based Drug Design
por: Thomas, Sherine E., et al.
Publicado: (2022)

Designing interactions by control of protein–ligand complex conformation: tuning arginine–arene interaction geometry for enhanced electrostatic protein–ligand interactions
por: Noresson, A.-L., et al.
Publicado: (2017)

A Ligand‐Directed Nitrophenol Carbonate for Transient in situ Bioconjugation and Drug Delivery
por: Burt, Anthony J., et al.
Publicado: (2020)

Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing
por: Patil, Rohan, et al.
Publicado: (2010)

Sliding tethered ligands add topological interactions to the toolbox of ligand–receptor design
por: Bauer, Martin, et al.
Publicado: (2015)

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density
por: Pearce, Nicholas M., et al.
Publicado: (2017)

Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions
por: Marsh, Lorraine
Publicado: (2011)

Alchemical absolute protein–ligand binding free energies for drug design
por: Khalak, Y., et al.
Publicado: (2021)

A General Ligand Design for Gold Catalysis allowing Ligand-Directed Anti Nucleophilic Attack of Alkynes
por: Wang, Yanzhao, et al.
Publicado: (2014)

Editorial: Chemoinformatics Approaches to Structure- and Ligand-Based Drug Design, Volume II
por: Ferreira, Leonardo L. G., et al.
Publicado: (2022)

A Mathematical Model for the Rational Design of Chimeric Ligands in Selective Drug Therapies
por: Doldán-Martelli, V, et al.
Publicado: (2013)

Data-Directed Drug Design
por: Hodgson, John
Publicado: (1991)

Editorial: Multi-Target-Directed Ligands (MTDL) as Challenging Research Tools in Drug Discovery: From Design to Pharmacological Evaluation
por: Alcaro, Stefano, et al.
Publicado: (2019)

Generating property-matched decoy molecules using deep learning
por: Imrie, Fergus, et al.
Publicado: (2021)

Designing and evaluating contextualized drug–drug interaction algorithms
por: Chou, Eric, et al.
Publicado: (2021)

Design and Synthesis of High Affinity Inhibitors of Plasmodium falciparum and Plasmodium vivax N-Myristoyltransferases Directed by Ligand Efficiency Dependent Lipophilicity (LELP)
por: Rackham, Mark D., et al.
Publicado: (2014)

Theoretical and experimental studies on the interaction of biphenyl ligands with human and murine PD-L1: Up-to-date clues for drug design
por: Donati, Greta, et al.
Publicado: (2023)

Sustainable Drug Discovery of Multi-Target-Directed Ligands for Alzheimer’s Disease
por: Rossi, Michele, et al.
Publicado: (2021)

Enhancing Ligand and Protein Sampling Using Sequential Monte Carlo
por: Suruzhon, Miroslav, et al.
Publicado: (2022)

Protein protein interactions, evolutionary rate, abundance and age
por: Saeed, Ramazan, et al.
Publicado: (2006)

Drug–Drug Interactions with Direct Oral Anticoagulants
por: Foerster, Kathrin I., et al.
Publicado: (2020)

Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics
por: Fusani, Lucia, et al.
Publicado: (2020)

Synergistic approach of structure-based and ligand-based drug design for the development of selective cannabinod receptor ligands
por: Günther, Robert, et al.
Publicado: (2012)

Controlling Intramolecular Interactions in the Design of Selective, High-Affinity Ligands for the CREBBP Bromodomain
por: Brand, Michael, et al.
Publicado: (2021)

Functionally guided alignment of protein interaction networks for module detection
por: Ali, Waqar, et al.
Publicado: (2009)

Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design
por: Chandramohan, Arun, et al.
Publicado: (2016)

Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study
por: Knapp, Bernhard, et al.
Publicado: (2014)

C3-Symmetric Ligands in Drug Design: When the Target Controls the Aesthetics of the Drug
por: Antonijevic, Mirjana, et al.
Publicado: (2023)

The Ligand for Osteoprotegerin (OPGL) Directly Activates Mature Osteoclasts
por: Burgess, Teresa L., et al.
Publicado: (1999)

Trastuzumab-Peptide Interactions: Mechanism and Application in Structure-Based Ligand Design
por: Sun, Tian-Yang, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_nocbg6m0b4bj1butcub3nml2pe