ArticleJournal of computer-aided molecular design2014
Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- Possible Thrombus-clearing Mechanism and Modification Suggestion of β-sitosterol.Current drug targets · 2026Article
- Improved Structure-Based Histidine pJournal of chemical information and modeling · 2025Article
- Action mechanism and molecular design of indolepyrrodione inhibitors targeting IDO1.Frontiers in molecular biosciences · 2025Article
- Molecular Dynamics Simulation of Lipid Nanoparticles Encapsulating mRNA.Molecules (Basel, Switzerland) · 2024Article
- Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools.Scientific reports · 2023Article
- Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold.Frontiers in molecular biosciences · 2023Article
- Solvated interaction energy: from small-molecule to antibody drug design.Frontiers in molecular biosciences · 2023Review
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
- Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.The Journal of chemical physics · 2021Article
- Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.Journal of computer-aided molecular design · 2018Article
- Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.The journal of physical chemistry. B · 2017Article
- Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.Journal of computer-aided molecular design · 2017Article
- Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.Journal of computer-aided molecular design · 2017Article
- Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).Journal of computer-aided molecular design · 2017Article
- Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.Journal of computer-aided molecular design · 2016Article
- BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.Journal of computer-aided molecular design · 2015Article
- Small-molecule inhibitors of the pseudaminic acid biosynthetic pathway: targeting motility as a key bacterial virulence factor.Antimicrobial agents and chemotherapy · 2014Article
- The SAMPL4 host-guest blind prediction challenge: an overview.Journal of computer-aided molecular design · 2014Review
- Blind prediction of HIV integrase binding from the SAMPL4 challenge.Journal of computer-aided molecular design · 2014Review
- Blind prediction of solvation free energies from the SAMPL4 challenge.Journal of computer-aided molecular design · 2014Review
Corrections and comments
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We continued prospective assessments of the Wilma-solvated interaction energy (SIE) platform for pose prediction, binding affinity prediction, and virtual screening on the challenging SAMPL4 data sets including the HIV-integrase inhibitor and two host-guest systems. New features of the docking algorithm and scoring function are tested here prospectively for the first time. Wilma-SIE provides good correlations with actual binding affinities over a wide range of binding affinities that includes strong binders as in the case of SAMPL4 host-guest systems. Absolute binding affinities are also reproduced with appropriate training of the scoring function on available data sets or from comparative estimation of the change in target's vibrational entropy. Even when binding modes are known, SIE predictions lack correlation with experimental affinities within dynamic ranges below 2 kcal/mol as in the case of HIV-integrase ligands, but they correctly signaled the narrowness of the dynamic range. Using a common protein structure for all ligands can reduce the noise, while incorporating a more sophisticated solvation treatment improves absolute predictions. The HIV-integrase virtual screening data set consists of promiscuous weak binders with relatively high flexibility and thus it falls outside of the applicability domain of the Wilma-SIE docking platform. Despite these difficulties, unbiased docking around three known binding sites of the enzyme resulted in over a third of ligands being docked within 2 Å from their actual poses and over half of the ligands docked in the correct site, leading to better-than-random virtual screening results.
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