ArticleJournal of molecular modeling2015
An approach to creating a more realistic working model from a protein data bank entry.
Article in Journal of molecular modeling, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability.Communications biology · 2024Article
- The in-silico evaluation of important GLUT9 residue for uric acid transport based on renal hypouricemia type 2.Chemico-biological interactions · 2023Article
- Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis.Journal of molecular modeling · 2022Article
- Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes.Nanomaterials (Basel, Switzerland) · 2022Article
- Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules.Journal of molecular modeling · 2020Article
- Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis.Nanomaterials (Basel, Switzerland) · 2020Article
- Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes.Journal of molecular modeling · 2019Article
- An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin.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
- Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.International journal of molecular sciences · 2016Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
An accurate model of three-dimensional protein structure is important in a variety of fields such as structure-based drug design and mechanistic studies of enzymatic reactions. While the entries in the Protein Data Bank ( http://www.pdb.org ) provide valuable information about protein structures, a small fraction of the PDB structures were found to contain anomalies not reported in the PDB file. The semiempirical PM7 method in MOPAC2012 was used for identifying anomalously short hydrogen bonds, C-H⋯O/C-H⋯N interactions, non-bonding close contacts, and unrealistic covalent bond lengths in recently published Protein Data Bank files. It was also used to generate new structures with these faults removed. When the semiempirical models were compared to those of PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/), the clashscores, as defined by MolProbity ( http://molprobity.biochem.duke.edu/), were better in about 50% of the structures. The semiempirical models also had a lower root-mean-square-deviation value in nearly all cases than those from PDB_REDO, indicative of a better conservation of the tertiary structure. Finally, the semiempirical models were found to have lower clashscores than the initial PDB file in all but one case. Because this approach maintains as much of the original tertiary structure as possible while improving anomalous interactions, it should be useful to theoreticians, experimentalists, and crystallographers investigating the structure and function of proteins.
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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.