ArticleCurrent pharmaceutical design2011
Molecular recognition in the case of flexible targets.
Article in Current pharmaceutical design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Microbial enzymes for plastic degradation: a comprehensive review of current status and emerging trends.Biodegradation · 2026Review
- From In Silico to a Cellular Model: Molecular Docking Approach to Evaluate Antioxidant Bioactive Peptides.Antioxidants (Basel, Switzerland) · 2023Review
- Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study.Journal of computer-aided molecular design · 2021Article
- Article
- Molecular Modeling Applied to the Discovery of New Lead Compounds for P2 Receptors Based on Natural Sources.Frontiers in pharmacology · 2020Review
- Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation.Structure (London, England : 1993) · 2019Article
- Drug search for leishmaniasis: a virtual screening approach by grid computing.Journal of computer-aided molecular design · 2016Article
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
- Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors.Memorias do Instituto Oswaldo Cruz · 2015Review
- Multiple Drug Transport Pathways through Human P-Glycoprotein.Biochemistry · 2015Article
- Structural basis of resistance to anti-cytochrome bc₁ complex inhibitors: implication for drug improvement.Current pharmaceutical design · 2014Review
- In silico mechanistic profiling to probe small molecule binding to sulfotransferases.PloS one · 2013Article
- Protein flexibility in virtual screening: the BACE-1 case study.Journal of chemical information and modeling · 2012Article
- Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery.Journal of computational chemistry · 2012Article
- Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites.Biochemistry · 2012Article
- Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein.Biochemistry · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
A protein's flexibility is well recognized to underlie its capacity to engage in critical functions, such as signal transduction, biomolecular transport and biochemical reactivity. Molecular recognition is also tightly linked to the dynamics of the binding partners, yet protein flexibility has largely been ignored by the growing field of structure-based drug design (SBDD). In combination with experimentally determined structures, a number of computational methods have been proposed to model protein movements, which may be important for small molecule binding. Such techniques have the ability to expose new binding site conformations, which may in turn recognize and lead to the discovery of more potent and selective drugs through molecular docking. In this article, we discuss various methods and focus on the Relaxed Complex Scheme (RCS), which uses Molecular Dynamics (MD) simulations to model full protein flexibility and enhance virtual screening programmes. We review practical applications of the RCS and use a recent study of the HIV-1 reverse transcriptase to illustrate the various phases of the scheme. We also discuss some encouraging developments, aimed at addressing current weaknesses of the RCS.
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