Exploration of interaction scoring criteria in the CANDO platform

Exploration of interaction scoring criteria in the CANDO platform

Abstract Objective Ascertain the optimal interaction scoring criteria for the Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun drug repurposing to improve benchmarking performance, thereby enabling more accurate prediction of novel therapeutic drug-indication pairs. Re...

Full description

Bibliographic Details
Main Authors:	Zackary Falls, William Mangione, James Schuler, Ram Samudrala
Format:	Article
Language:	English
Published:	BMC 2019-06-01
Series:	BMC Research Notes
Subjects:	Drug repurposing Drug-protein interaction Binding site similarity Protein structure docking Molecular fingerprinting
Online Access:	http://link.springer.com/article/10.1186/s13104-019-4356-3

Similar Items

Optimal COVID-19 therapeutic candidate discovery using the CANDO platform
by: William Mangione, et al.
Published: (2022-08-01)

Combating Ebola with Repurposed Therapeutics Using the CANDO Platform
by: Gaurav Chopra, et al.
Published: (2016-11-01)

Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform
by: Matthew L. Hudson, et al.
Published: (2021-04-01)

Effective holistic characterization of small molecule effects using heterogeneous biological networks
by: William Mangione, et al.
Published: (2023-04-01)

LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds
by: Faraz Shaikh, et al.
Published: (2021-06-01)

Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities
by: Beihong Ji, et al.
Published: (2021-02-01)

A Deep-Learning Proteomic-Scale Approach for Drug Design
by: Brennan Overhoff, et al.
Published: (2021-12-01)

TWN-RENCOD: A novel method for protein binding site comparison
by: Kwang-Eun Choi, et al.
Published: (2023-01-01)

Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
by: Ozren Jović, et al.
Published: (2021-07-01)

Repurposing Amphotericin B: anti-microbial, molecular docking and molecular dynamics simulation studies suggest inhibition potential of Amphotericin B against MRSA
by: Neha Farid, et al.
Published: (2023-06-01)

Structural Bioinformatics and Protein Docking Analysis of the Molecular Chaperone-Kinase Interactions: Towards Allosteric Inhibition of Protein Kinases by Targeting the Hsp90-Cdc37 Chaperone Machinery
by: Gennady Verkhivker, et al.
Published: (2013-11-01)

Systematic Studies on the Protocol and Criteria for Selecting a Covalent Docking Tool
by: Chang Wen, et al.
Published: (2019-06-01)

Uncovering New Drug Properties in Target-Based Drug–Drug Similarity Networks
by: Lucreţia Udrescu, et al.
Published: (2020-09-01)

Accelerating Drug Discovery by Early Protein Drug Target Prediction Based on a Multi-Fingerprint Similarity Search <sup>†</sup>
by: Michele Montaruli, et al.
Published: (2019-06-01)

Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints
by: Jie Liu, et al.
Published: (2017-07-01)

Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease
by: Manoj J. Mammen, et al.
Published: (2022-05-01)

Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing
by: James Schuler, et al.
Published: (2019-10-01)

Targeting envelope proteins of poxviruses to repurpose phytochemicals against monkeypox: An in silico investigation
by: Pallavi Gulati, et al.
Published: (2023-01-01)

Computational Screening of Repurposed Drugs Targeting Sars-Cov-2 Main Protease By Molecular Docking
by: Yow Hui Yin, et al.
Published: (2022-09-01)

Prediction of protein-binding areas by small-world residue networks and application to docking
by: Glaser Fabian, et al.
Published: (2011-09-01)

PLATO: A Predictive Drug Discovery Web Platform for Efficient Target Fishing and Bioactivity Profiling of Small Molecules
by: Fulvio Ciriaco, et al.
Published: (2022-05-01)

Repurposing of anticancer drugs: in vitro and in vivo activities against Schistosoma mansoni
by: Noemi Cowan, et al.
Published: (2015-08-01)

Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities
by: Jieyi Di, et al.
Published: (2019-10-01)

Repurposing of thermally stable nucleic-acid aptamers for targeting tetrodotoxin (TTX)
by: Yuanyuan Li, et al.
Published: (2022-01-01)

Fluoropyrimidines affect de novo pyrimidine synthesis impairing biofilm formation in Escherichia coli
by: Srikanth Ravishankar, et al.
Published: (2024-06-01)

Computational Drug Repurposing Based on a Recommendation System and Drug–Drug Functional Pathway Similarity
by: Mengting Shao, et al.
Published: (2022-02-01)

InContext: curation of medical context for drug indications
by: Kody Moodley, et al.
Published: (2021-02-01)

Comparative assessment of strategies to identify similar ligand-binding pockets in proteins
by: Rajiv Gandhi Govindaraj, et al.
Published: (2018-03-01)

In silico identification of drug candidates against COVID-19
by: Yifei Wu, et al.
Published: (2020-01-01)

Drug Repurposing and De Novo Drug Discovery of Protein Kinase Inhibitors as New Drugs against Schistosomiasis
by: Bernardo Pereira Moreira, et al.
Published: (2022-02-01)

Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery
by: Crhisllane Rafaele dos Santos Vasconcelos, et al.
Published: (2021-04-01)

Characterizations and molecular docking mechanism of the interactions between peptide FDGDF (Phe-Asp-Gly-Asp-Phe) and SOD enzyme
by: C.H.E.N. Wen-Tao, et al.
Published: (2024-01-01)

A Maximum Flow-Based Approach to Prioritize Drugs for Drug Repurposing of Chronic Diseases
by: Md. Mohaiminul Islam, et al.
Published: (2021-10-01)

Inhibition of Microtubule Affinity Regulating Kinase 4 by Metformin: Exploring the Neuroprotective Potential of Antidiabetic Drug through Spectroscopic and Computational Approaches
by: Ghulam Md. Ashraf, et al.
Published: (2022-07-01)

Exploration of key drug target proteins highlighting their related regulatory molecules, functional pathways and drug candidates associated with delirium: evidence from meta-data analyses
by: Md Parvez Mosharaf, et al.
Published: (2023-11-01)

Repurposing Known Drugs as Covalent and Non-covalent Inhibitors of the SARS-CoV-2 Papain-Like Protease
by: Pietro Delre, et al.
Published: (2020-11-01)

FingerDTA: A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction
by: Xuekai Zhu, et al.
Published: (2023-03-01)

Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products
by: Steve O’Hagan, et al.
Published: (2020-11-01)

Evaluating cepharanthine analogues as natural drugs against SARS‐CoV‐2
by: Atsushi Hijikata, et al.
Published: (2022-01-01)

Design of Potential Anti-Leishmanial Pharmacophores via In Silico Drug Repurposing
by: Sana Ahdeno, et al.
Published: (2020-10-01)