ArticlePhysical chemistry chemical physics : PCCP2014
Current and emerging opportunities for molecular simulations in structure-based drug design.
Article in Physical chemistry chemical physics : PCCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Deciphering the rules of regulated cell death subroutines by in silico methods.Journal of advanced research · 2026Review
- Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators.Communications chemistry · 2023Article
- On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies.Journal of chemical theory and computation · 2021Article
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies.Journal of computer-aided molecular design · 2019Article
- Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases.International journal of molecular sciences · 2019Review
- Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Article
- Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.Journal of computer-aided molecular design · 2018Article
- Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.Journal of computer-aided molecular design · 2017Article
- Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations.Physical chemistry chemical physics : PCCP · 2016Article
- Blinded predictions of distribution coefficients in the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
- Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2.PLoS computational biology · 2015Article
- Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.The journal of physical chemistry. B · 2015Article
- An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald.The Journal of chemical physics · 2014Article
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Abstract
An overview of the current capabilities and limitations of molecular simulation of biomolecular complexes in the context of computer-aided drug design is provided. Steady improvements in computer hardware coupled with more refined representations of energetics are leading to a new appreciation of the driving forces of molecular recognition. Molecular simulations are poised to more frequently guide the interpretation of biophysical measurements of biomolecular complexes. Ligand design strategies emerge from detailed analyses of computed structural ensembles. The feasibility of routine applications to ligand optimization problems hinges upon successful extensive large scale validation studies and the development of protocols to intelligently automate computations.
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