Chemical Similarity Searching
TL;DR: The concept of similarity searching is introduced, differentiating it from the more common substructure searching, and the current generation of fragment-based measures that are used for searching chemical structure databases are discussed.
read more
Abstract: This paper reviews the use of similarity searching in chemical databases. It begins by introducing the concept of similarity searching, differentiating it from the more common substructure searching, and then discusses the current generation of fragment-based measures that are used for searching chemical structure databases. The next sections focus upon two of the principal characteristics of a similarity measure: the coefficient that is used to quantify the degree of structural resemblance between pairs of molecules and the structural representations that are used to characterize molecules that are being compared in a similarity calculation. New types of similarity measure are then compared with current approaches, and examples are given of several applications that are related to similarity searching.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor
Rui Duan,Xianjin Xu,Xiaoqin Zou +2 more
TL;DR: D3R 2016 Grand Challenge 2 focused on predictions of binding modes and affinities for 102 compounds against the farnesoid X receptor (FXR), and an in-house knowledge-based scoring function ITScore2 and MM/PBSA approach were employed for the binding affinity prediction.
12
Bioassay-Guided Interpretation of Antimicrobial Compounds in Kumu, a TCM Preparation From Picrasma quassioides’ Stem via UHPLC-Orbitrap-Ion Trap Mass Spectrometry Combined With Fragmentation and Retention Time Calculation
Haibo Hu,Changling Hu,Jinnian Peng,Alokesh Kumar Ghosh,Ajmal Khan,Dan Sun,Dan Sun,Walter Luyten +7 more
TL;DR: In this article, two types of columns (normal and reverse-phase) were used for speedy bioassay-guided isolation from Kumu, and the active peaks were collected and identified via an UHPLC-Orbitrap-Ion Trap Mass Spectrometer, combined with MS Fragmenter and ChromGenius.
Fragment-Based Prediction of Cytochromes P450 2D6 and 1A2 Inhibition by Recursive Partitioning
TL;DR: A method to build predictive and interpretable models for the prediction of cytochrome P450 (CYP) 1A2 and 2D6 inhibition using recursive partitioning (RP), a well-known technique for the construction of decision trees.
12
Analysis of structure-Caco-2 permeability relationships using a property landscape approach.
TL;DR: This work characterized systematically the Caco-2 permeability landscape of a benchmark dataset of 100 molecules using a novel approach based on the emerging concept of property landscape modeling and introduced the concept of “permeability cliffs” discussing cases of compounds with high molecular similarity but large permeability difference.
12
Efficient Discovery of Visible Light-Activated Azoarene Photoswitches with Long Half-Lives Using Active Search.
Fatemah Mukadum,Quan Nguyen,Daniel Adrion,Gabriel Appleby,Rui Chen,Haley Dang,Remco Chang,Roman Garnett,Steven A. Lopez +8 more
TL;DR: In this article, the authors applied active search, a machine-learning technique, to intelligently search a chemical search space of 255 991 photoswitches based on 29 known azoarenes and their derivatives.
12
References
Hierarchical Grouping to Optimize an Objective Function
TL;DR: In this paper, a procedure for forming hierarchical groups of mutually exclusive subsets, each of which has members that are maximally similar with respect to specified characteristics, is suggested for use in large-scale (n > 100) studies when a precise optimal solution for a specified number of groups is not practical.
19.8K
Features of Similarity
TL;DR: The metric and dimensional assumptions that underlie the geometric representation of similarity are questioned on both theoretical and empirical grounds and a set of qualitative assumptions are shown to imply the contrast model, which expresses the similarity between objects as a linear combination of the measures of their common and distinctive features.
Development and validation of a genetic algorithm for flexible docking.
TL;DR: GOLD (Genetic Optimisation for Ligand Docking) is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding.
6.5K
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins.
TL;DR: The main features of the CoMFA approach, exemplified by analyses of the affinities of 21 varied steroids to corticosteroid and testosterone-binding globulins, and a number of advances in the methodology of molecular graphics are described.
3.8K
A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
2.8K