Modeling of loops in protein structures

Keywords

Dihedral angle, Loop (graph theory), Loop modeling, Superposition principle, Molecular dynamics

References

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• Role of loops in the folding and stability of yeast phosphoglycerate kinase.Bruno Collinet, Pascal Garcia, Philippe Minard — 2001
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• Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational searchRuben Abagyan, Serge Batalov, Timothy Cardozo — 1997
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Cited by

• Motion Planning Algorithms for General Closed-Chain MechanismsJuan Cortés — 2003
• Statistical potentials for fold assessmentEzio Santagata, Davide Dalmazzo, Lucia Tsantilis — 2002
• Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing充 多田 — 2004
• Identification of function-associated loop motifs and application to protein function predictionJordi Espadaler, Enrique Querol, Francesc Avilés — 2006
• Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase.Zhaofeng Ding, Huachun Wang, Xiangyang Liang — 2007
• Model Structure of Human APOBEC3GKatie Kitamura — 2007
• The role of protein 3D-structures in the drug discovery process.Alexander Hillisch, Rolf Hilgenfeld — 2003
• Analysis of the CYP51 gene and encoded protein in propiconazole-resistant isolates of Mycosphaerella fijiensis.Sang H. Son, Yu-Mi Kim — 2009
• Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics studyElad Eliahoo, Ron Ben Yosef, Laura Pérez‐Cano — 2010
• RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.Jorun Høier Kjølaas — 2010
• AWSEM-MD: Protein Structure Prediction Using Coarse-grained Physical Potentials and Bioinformatically Based Local Structure BiasingJeong‐Hwan Park, U Hyo-Seop, Jong-Geun Pyeon — 2012
• Multicofactor proteins: structure,prediction, functionS. Hearnshaw — 2011
• pH‐sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stabilityManuel Perea, Salvador Algarabel González — 2013
• Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop predictionCarlos Arrizabalaga — 2014
• Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forestMariana Arghir, Adrian Leu — 2015
• In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139成子 黒田 — 2015
• An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native PigsПлотникова Алена Владимировна — 2016
• Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1.McHugh Ga, Karen Luker, Campbell Mg — 2016
• Molecular Modelling of G Protein‐Coupled Receptors Through the WebPatricia Moraga Barrero — 2012
• Characterization of phosphate transporter(s) and understanding their role in Leishmania donovani parasiteR. W. Marsh, J. G. Maynard — 2018

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