ArticleProteins2013
3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
Article in Proteins, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Protein Structure Prediction Methods.Advances in experimental medicine and biology · 2026Review
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- Promising antiviral inhibitors against lumpy skin disease: A vetinformatics approach.Open veterinary journal · 2024Article
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- Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from Influenza Like Illness (ILI) and Severe Acute Respiratory Illness (SARI) cases reported between July-December, 2022.Scientific reports · 2024Article
- Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape.International journal of molecular sciences · 2024Article
- AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape.Journal of chemical information and modeling · 2024Article
- Structure based docking and biological evaluation towards exploring potential anti-cancerous and apoptotic activity of 6-Gingerol against human prostate carcinoma cells.BMC complementary medicine and therapies · 2024Article
- Characterization of novel CD19-specific VHHs isolated from a camelid immune library by phage display.Journal of translational medicine · 2023Article
- In Silico Physicochemical Characterization of Fusion Proteins from Emerging Amazonian Arboviruses.Life (Basel, Switzerland) · 2023Article
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- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Weak Noncovalent Interactions in Three Closely Related Adamantane-Linked 1,2,4-TriazoleMolecules (Basel, Switzerland) · 2022Article
- Commonly used surfactants sodium dodecyl sulphate, cetylpyridinium chloride and sodium laureth sulphate and their effects on antioxidant defence system and oxidative stress indices in Cyprinus carpio L.: an integrated in silico and in vivo approach.Environmental science and pollution research international · 2022Article
- Characterization and Structural Prediction of Proteins in SARS-CoV-2 Bangladeshi Variant Through Bioinformatics.Microbiology insights · 2022Article
- Molecular Modeling of Subtype-Specific Tat Protein Signatures to Predict Tat-TAR Interactions That May Be Involved in HIV-Associated Neurocognitive Disorders.Frontiers in microbiology · 2022Article
- In vitro and in silico analysis reveals antifungal activity and potential targets of curcumin on Paracoccidioides spp.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2021Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
One of the major limitations of computational protein structure prediction is the deviation of predicted models from their experimentally derived true, native structures. The limitations often hinder the possibility of applying computational protein structure prediction methods in biochemical assignment and drug design that are very sensitive to structural details. Refinement of these low-resolution predicted models to high-resolution structures close to the native state, however, has proven to be extremely challenging. Thus, protein structure refinement remains a largely unsolved problem. Critical assessment of techniques for protein structure prediction (CASP) specifically indicated that most predictors participating in the refinement category still did not consistently improve model quality. Here, we propose a two-step refinement protocol, called 3Drefine, to consistently bring the initial model closer to the native structure. The first step is based on optimization of hydrogen bonding (HB) network and the second step applies atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields. The approach has been evaluated on the CASP benchmark data and it exhibits consistent improvement over the initial structure in both global and local structural quality measures. 3Drefine method is also computationally inexpensive, consuming only few minutes of CPU time to refine a protein of typical length (300 residues). 3Drefine web server is freely available at http://sysbio.rnet.missouri.edu/3Drefine/.
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