ArticleProteins2013
Toward optimal fragment generations for ab initio protein structure assembly.
Article in Proteins, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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Who cites it
103 citing papers in PubMed.
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- Structural Space of the Duffy Antigen/Receptor for Chemokines' Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
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- Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor.Nature communications · 2023Article
- Binding by calmodulin is coupled to transient unfolding of the third FF domain of Prp40A.Protein science : a publication of the Protein Society · 2023Article
- Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins.International journal of molecular sciences · 2023Article
- De novo protein fold design through sequence-independent fragment assembly simulations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- PPDPF Promotes the Development of Mutant KRAS-Driven Pancreatic Ductal Adenocarcinoma by Regulating the GEF Activity of SOS1.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Functional Testing of Bone Morphogenetic Protein (BMP) Pathway Variants Identified on Whole-Exome Sequencing in a Patient with Delayed-Onset Fibrodysplasia Ossificans Progressiva (FOP) Using ACVR1Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2022Article
- Acetylated HOXB13 Regulated Super Enhancer Genes Define Therapeutic Vulnerabilities of Castration-Resistant Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Biocomputational Assessment of Natural Compounds as a Potent Inhibitor to Quorum Sensors inMolecules (Basel, Switzerland) · 2022Article
- Equilibrium Between Dimeric and Monomeric Forms of Human Epidermal Growth Factor is Shifted Towards Dimers in a Solution.The protein journal · 2022Article
- Dimerization Activity of a Disordered N-Terminal Domain fromInternational journal of molecular sciences · 2022Article
- Proteomic Tools for the Analysis of Cytoskeleton Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational Structural and Functional Analyses of ORF10 in Novel Coronavirus SARS-CoV-2 Variants to Understand Evolutionary Dynamics.Evolutionary bioinformatics online · 2022Article
- Visualising Viruses.The Journal of general virology · 2022Review
43 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Fragment assembly using structural motifs excised from other solved proteins has shown to be an efficient method for ab initio protein-structure prediction. However, how to construct accurate fragments, how to derive optimal restraints from fragments, and what the best fragment length is are the basic issues yet to be systematically examined. In this work, we developed a gapless-threading method to generate position-specific structure fragments. Distance profiles and torsion angle pairs are then derived from the fragments by statistical consistency analysis, which achieved comparable accuracy with the machine-learning-based methods although the fragments were taken from unrelated proteins. When measured by both accuracies of the derived distance profiles and torsion angle pairs, we come to a consistent conclusion that the optimal fragment length for structural assembly is around 10, and at least 100 fragments at each location are needed to achieve optimal structure assembly. The distant profiles and torsion angle pairs as derived by the fragments have been successfully used in QUARK for ab initio protein structure assembly and are provided by the QUARK online server at http://zhanglab.ccmb. med.umich.edu/QUARK/.
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