ArticleJournal of chemical information and modeling2014
Dihedral-based segment identification and classification of biopolymers I: proteins.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Binding of Urinary Human Serum Albumin Fragments to Albumin-Selective Aptamer-Bound Graphene Quantum Dots: Simulation Studies.Langmuir : the ACS journal of surfaces and colloids · 2025Article
- Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.Molecules (Basel, Switzerland) · 2023Article
- Structural basis ofeLife · 2022Article
- Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity.Journal of chemical theory and computation · 2021Article
- Assigning secondary structure in proteins using AI.Journal of molecular modeling · 2021Article
- A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy.Communications biology · 2020Article
- How accurate is circular dichroism-based model validation?European biophysics journal : EBJ · 2020Article
- Fluorescence-Labeled Amyloid Beta Monomer: A Molecular Dynamical Study.Molecules (Basel, Switzerland) · 2020Article
- Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank.Frontiers in molecular biosciences · 2019Article
- A cation-π interaction in a transmembrane helix of vacuolar ATPase retains the proton-transporting arginine in a hydrophobic environment.The Journal of biological chemistry · 2018Article
- MDplot: Visualise Molecular Dynamics.The R journal · 2017Article
- Article
- Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting.Journal of chemical information and modeling · 2016Article
- Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area.Scientific reports · 2016Article
- A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.International journal of molecular sciences · 2016Article
- Article
- Amino Acids in Nine Ligand-Prefer Ramachandran Regions.BioMed research international · 2015Article
- Dihedral-based segment identification and classification of biopolymers II: polynucleotides.Journal of chemical information and modeling · 2014Article
- Dihedral-based segment identification and classification of biopolymers I: proteins.Journal of chemical information and modeling · 2014Article
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2 authors.
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Abstract
A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.
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