ArticleJournal of chemical information and modeling2011
A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series.
Article in Journal of chemical information and modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Action mechanism and molecular design of indolepyrrodione inhibitors targeting IDO1.Frontiers in molecular biosciences · 2025Article
- Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.Journal of computer-aided molecular design · 2022Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.Journal of computer-aided molecular design · 2022Article
- Modeling receptor flexibility in the structure-based design of KRASJournal of computer-aided molecular design · 2022Article
- PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions.Communications biology · 2021Article
- Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations.Journal of computer-aided molecular design · 2021Article
- SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2021Article
- SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.Journal of computer-aided molecular design · 2021Article
- Tetrahydroisoquinoline CXCR4 Antagonists Adopt a Hybrid Binding Mode within the Peptide Subpocket of the CXCR4 Receptor.ACS medicinal chemistry letters · 2019Article
- Energetic differences between non-domain-swapped and domain-swapped chain connectivities in the K2P potassium channel TRAAK.RSC advances · 2018Article
- Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations.Communications biology · 2018Article
- Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation.ChemMedChem · 2017Article
- Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58.Biochemistry · 2014Article
- Article
- A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection.Antimicrobial agents and chemotherapy · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
We introduce the "Prime-ligand" method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are "docked" by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Data Bank and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and the experimental data for cases in which binding affinities differ by at least 1 order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol because of the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligands bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligands in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.