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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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Book ChapterDOI

Molegro Virtual Docker for Docking

TL;DR: A tutorial to carry out docking simulations with MVD and how to perform a statistical analysis of the docking results with the program SAnDReS is described and the redocking simulation focused the cyclin-dependent kinase 2 in complex with a competitive inhibitor is described.
Journal ArticleDOI

RNA-modifying proteins as anticancer drug targets.

TL;DR: The current understanding of RNA modifications with a focus on mRNA methylation is examined, their possible roles in specific cancer indications are highlighted and the emerging potential of RNA-modifying proteins as therapeutic targets is discussed.
Journal ArticleDOI

Recent applications of machine learning in medicinal chemistry.

TL;DR: In this review, examples of recent developments in machine learning application are described, which have the potential to impact different parts of the drug discovery and development flow scheme.
Journal ArticleDOI

Machine Learning in Chemical Engineering: Strengths, Weaknesses, Opportunities, and Threats

TL;DR: The greatest opportunities involve using machine learning in time-limited applications such as real-time optimization and planning that require high accuracy and that can build on models with a self-learning ability to recognize patterns, learn from data, and become more intelligent over time.
Journal Article

Well-tempered metadynamics: a smoothly-converging and tunable free-energy method

TL;DR: In this paper, a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias is presented, which is tested on the reconstruction of an alanine dipeptide free energy landscape.
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

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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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