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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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Book ChapterDOI

Van der Waals Potential in Protein Complexes.

TL;DR: The Lennard-Jones potential and its application to calculate potential energy for an ensemble of structures is described to highlight the main features related to the importance of this interaction for binding affinity.
Journal ArticleDOI

Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated by 1H NMR and All-Atom Molecular Dynamics Simulations

TL;DR: The findings from this study illustrate that 1H NMR and AA-MD simulations can be useful, complementary tools in early evaluation of aggregation propensity and formulation development for peptide drugs.
Book ChapterDOI

Challenges for the Optimization of Drug Therapy in the Treatment of Cancer

TL;DR: In this paper, the authors discuss the challenges for personalized oncology to take off and present an approach based on hub inhibition that they are developing, where the subtraction of RNA-seq data of tumoral and non-tumoral surrounding tissues in biopsies allows the identification of up-regulated genes in tumors of patients.
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Structure-based discovery and bio-evaluation of a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one as a phosphodiesterase 10A inhibitor

TL;DR: The identification of a new PDE10A inhibitor is described by structure-based virtual screening combining pharmacophore modelling, molecular docking, molecular dynamics simulations, and biological evaluation and the novel scaffold of Zinc42657360 can be used for the rational design of PDE 10A inhibitors with improved affinity.
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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