ArticleJournal of computer-aided molecular design2014
Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4.
Article in Journal of computer-aided molecular design, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 25 citations in OpenAlex.
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- Structure based prediction of a novel GPR120 antagonist based on pharmacophore screening and molecular dynamics simulations.Computational and structural biotechnology journal · 2021Article
- Best Practices for Alchemical Free Energy Calculations [Article v1.0].Living journal of computational molecular science · 2020Article
- Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor ofACS infectious diseases · 2019Article
- Chemoinformatics and structural bioinformatics in OCaml.Journal of cheminformatics · 2019Article
- Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.The journal of physical chemistry. B · 2018Article
- Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015.Journal of computer-aided molecular design · 2016Article
- Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future.Acta crystallographica. Section F, Structural biology communications · 2015Review
- A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.Journal of chemical information and modeling · 2015Article
- Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.Journal of computer-aided molecular design · 2014Article
- Blind prediction of HIV integrase binding from the SAMPL4 challenge.Journal of computer-aided molecular design · 2014Review
- SAMPL4 & DOCK3.7: lessons for automated docking procedures.Journal of computer-aided molecular design · 2014Article
- In silico, in vitro and cellular analysis with a kinome-wide inhibitor panel correlates cellular LRRK2 dephosphorylation to inhibitor activity on LRRK2.Frontiers in molecular neuroscience · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The SAMPL challenges provide an ideal opportunity for unbiased evaluation and comparison of different approaches used in computational drug design. During the fourth round of this SAMPL challenge, we participated in the virtual screening and binding pose prediction on inhibitors targeting the HIV-1 integrase enzyme. For virtual screening, we used well known and widely used in silico methods combined with personal in cerebro insights and experience. Regular docking only performed slightly better than random selection, but the performance was significantly improved upon incorporation of additional filters based on pharmacophore queries and electrostatic similarities. The best performance was achieved when logical selection was added. For the pose prediction, we utilized a similar consensus approach that amalgamated the results of the Glide-XP docking with structural knowledge and rescoring. The pose prediction results revealed that docking displayed reasonable performance in predicting the binding poses. However, prediction performance can be improved utilizing scientific experience and rescoring approaches. In both the virtual screening and pose prediction challenges, the top performance was achieved by our approaches. Here we describe the methods and strategies used in our approaches and discuss the rationale of their performances.
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