ArticleProteins2015
Accuracy issues involved in modeling in vivo protein structures using PM7.
Article in Proteins, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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Who cites it
8 citing papers in PubMed.
- Gas phase hydrolysis of organic sulfuric anhydride: the possibility and atmospheric influence in initial new particle formation.RSC advances · 2026Article
- A complex interplay of genetic introgression and local adaptation during the evolutionary history of three closely related spruce species.Plant diversity · 2025Article
- Quantum Mechanical Assessment of Protein-Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory.International journal of molecular sciences · 2023Article
- An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin.Journal of molecular modeling · 2017Article
- Understanding weakly coordinating anions: tetrakis(pentafluorophenyl)borate paired with inorganic and organic cations.Journal of molecular modeling · 2017Article
- Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.Advances in bioinformatics · 2017Article
- A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1.Journal of molecular modeling · 2016Article
- A comparison of X-ray and calculated structures of the enzyme MTH1.Journal of molecular modeling · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Using the semiempirical method PM7, an attempt has been made to quantify the error in prediction of the in vivo structure of proteins relative to X-ray structures. Three important contributory factors are the experimental limitations of X-ray structures, the difference between the crystal and solution environments, and the errors due to PM7. The geometries of 19 proteins from the Protein Data Bank that had small R values, that is, high accuracy structures, were optimized and the resulting drop in heat of formation was calculated. Analysis of the changes showed that about 10% of this decrease in heat of formation was caused by faults in PM7, the balance being attributable to the X-ray structure and the difference between the crystal and solution environments. A previously unknown fault in PM7 was revealed during tests to validate the geometries generated using PM7. Clashscores generated by the Molprobity molecular mechanics structure validation program showed that PM7 was predicting unrealistically close contacts between nonbonding atoms in regions where the local geometry is dominated by very weak noncovalent interactions. The origin of this fault was traced to an underestimation of the core-core repulsion between atoms at distances smaller than the equilibrium distance.
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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.