Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom

DOI10.1016/J.JTBI.2016.03.029MaRDI QIDQ738564zbMATH OpenOpenAlexWikidataFDO

Authors Avdesh Mishra, Sumaiya Iqbal, Md Tamjidul Hoque

Publication date 5 September 2016

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2016.03.029

zbMATH Keywords

optimizationgenetic algorithmprotein structure predictiondecoy structurenative structure

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Software, source code, etc. for problems pertaining to biology (92-04) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Recommendations

• Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold
• Some remarks on protein attribute prediction and pseudo amino acid composition
• Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern
• Novel scales based on hydrophobicity indices for secondary protein structure
• Application of density similarities to predict membrane protein types based on pseudo-amino acid composition

Cites work

• Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom
• Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network model
• Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou's general PseAAC
• Prediction of \(\beta\)-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine
• Some remarks on protein attribute prediction and pseudo amino acid composition

Cited in

(4)

• Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom
• 3DIGARS
• Fold recognition using the OPLS all-atom potential and the surface generalized Born solvent model
• CBSF: a new empirical scoring function for docking parameterized by weights of neural network

Describes a project that uses

Uses Software

• CHARMM
• PredLactamase
• I-TASSER
• SCWRL4
• iPro54-PseKNC
• iPPI-Esml
• iDNA-Methyl
• iRSpot-PseDNC
• iCTX-Type
• iNitro-Tyr

This page was built for publication: Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q738564)