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Open AccessJournal ArticleDOI

Computational methods in drug discovery.

TLDR
An overview of computational methods used in different facets of drug discovery and highlight some of the recent successes is presented, both structure-based and ligand-based drug discovery methods are discussed.
Abstract
The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.

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Citations
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Journal ArticleDOI

The role of alternative toxicological trials in drug discovery programs: The case of Caenorhabditis elegans and other methods.

TL;DR: This work presents a review of the literature published between the years 2000 and 2021 of in vivo alternative methods of toxicity screening employed in medicinal chemistry, which it is believed will be useful because, in addition to shortening research times, these studies provide much additional information aside from the toxicity of drug candidate compounds.
Book ChapterDOI

Ligand-Based Designing of Natural Products

TL;DR: This chapter discusses ligand-based designing of naturally available anticarcinogenic molecules, which are based on physicochemical properties and quantitative structure activity relationships of Curcumin and polyphenolic compounds.
Journal ArticleDOI

Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C

TL;DR: In this article , the authors used adaptive steered molecular dynamics (ASMD) and thermodynamic integration (TI) to estimate the calcium binding affinity of the cardiac troponin protein complex (cTn) subunit.
Journal ArticleDOI

Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies

Davide Bassani, +1 more
- 01 May 2023 - 
TL;DR: A brief overview of computational methods for drug discovery can be found in this article , focusing on their application in different scenarios of pharmaceutical and biological interest, not only highlighting their great potential and their benefits, but also discussing their actual limitations and eventual weaknesses.
Journal ArticleDOI

MultiPharm-DT: A Multi-Objective Decision Tool for Ligand-Based Virtual Screening Problems

TL;DR: This work proposes a new multi-objective methodology called MultiPharm-DT where several descriptors are considered si-multaneously and whose results are offered to the decision-maker without effort on their part and without relying on their expertise.
References
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Journal ArticleDOI

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.

疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

宁北芳, +1 more
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI

Scalable molecular dynamics with NAMD

TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Journal ArticleDOI

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

TL;DR: Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described in this article, where the rule of 5 is used to predict poor absorption or permeability when there are more than 5 H-bond donors, 10 Hbond acceptors, and the calculated Log P (CLogP) is greater than 5 (or MlogP > 415).
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