Binding site detection and druggability prediction of protein targets for structure-based drug design
Assessing whether a protein structure is a good target or not before actually doing structure-
based drug design on it is an important step to speed up the ligand discovery process. This …
based drug design on it is an important step to speed up the ligand discovery process. This …
Identifying and characterizing binding sites and assessing druggability
TA Halgren - Journal of chemical information and modeling, 2009 - ACS Publications
Identification and characterization of binding sites is key in the process of structure-based
drug design. In some cases there may not be any information about the binding site for a …
drug design. In some cases there may not be any information about the binding site for a …
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction
Y Xu, S Wang, Q Hu, S Gao, X Ma, W Zhang… - Nucleic acids …, 2018 - academic.oup.com
CavityPlus is a web server that offers protein cavity detection and various functional
analyses. Using protein three-dimensional structural information as the input, CavityPlus …
analyses. Using protein three-dimensional structural information as the input, CavityPlus …
De novo design: balancing novelty and confined chemical space
Importance of the field: De novo drug design serves as a tool for the discovery of new
ligands for macromolecular targets as well as optimization of known ligands. Recently …
ligands for macromolecular targets as well as optimization of known ligands. Recently …
Computational approaches to identifying and characterizing protein binding sites for ligand design
Given the three‐dimensional structure of a protein, how can one find the sites where other
molecules might bind to it? Do these sites have the properties necessary for high affinity …
molecules might bind to it? Do these sites have the properties necessary for high affinity …
AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
We report here a robust automated active site detection, docking, and scoring (AADS)
protocol for proteins with known structures. The active site finder identifies all cavities in a …
protocol for proteins with known structures. The active site finder identifies all cavities in a …
Rfdt: A rotation forest-based predictor for predicting drug-target interactions using drug structure and protein sequence information
Background: Identification of interaction between drugs and target proteins plays an
important role in discovering new drug candidates. However, through the experimental …
important role in discovering new drug candidates. However, through the experimental …
Prediction of drug–target interaction networks from the integration of protein sequences and drug chemical structures
Knowledge of drug–target interaction (DTI) plays an important role in discovering new drug
candidates. Unfortunately, there are unavoidable shortcomings; including the time …
candidates. Unfortunately, there are unavoidable shortcomings; including the time …
Drug-like density: a method of quantifying the “bindability” of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank
RP Sheridan, VN Maiorov, MK Holloway… - Journal of chemical …, 2010 - ACS Publications
One approach to estimating the “chemical tractability” of a candidate protein target where we
know the atomic resolution structure is to examine the physical properties of potential …
know the atomic resolution structure is to examine the physical properties of potential …
Lessons for fragment library design: analysis of output from multiple screening campaigns
Over the past 8 years, we have developed, refined and applied a fragment based discovery
approach to a range of protein targets. Here we report computational analyses of various …
approach to a range of protein targets. Here we report computational analyses of various …