MODELLER

MODELLER: A Program for Protein Structure Modeling. MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac. Several graphical interfaces to MODELLER are commercially available. There are also many other resources and people using Modeller in graphical or web interfaces or other frameworks.


References in zbMATH (referenced in 33 articles )

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  1. Tanwer, Pooja; Kolora, Sree Rohit Raj; Babbar, Anshu; Saluja, Daman; Chaudhry, Uma: Identification of potential therapeutic targets in \textitNeisseriagonorrhoeae by an \textitin-silico approach (2020)
  2. Rout, Subhashree; Mahapatra, Rajani Kanta: \textitInsilico analysis of \textitplasmodiumfalciparum CDPK5 protein through molecular modeling, docking and dynamics (2019)
  3. Penner, R. C.: Moduli spaces and macromolecules (2016)
  4. Samal, Himanshu Bhusan; Prava, Jyoti; Suar, Mrutyunjay; Mahapatra, Rajani Kanta: Comparative genomics study of \textitSalmonellaTyphimurium LT2 for the identification of putative therapeutic candidates (2015)
  5. Dorn, Márcio; Buriol, Luciana S.; Lamb, Luis C.: MOIRAE: a computational strategy to extract and represent structural information from experimental protein templates (2014) ioport
  6. Nezafat, Navid; Ghasemi, Younes; Javadi, Gholamreza; Khoshnoud, Mohammad Javad; Omidinia, Eskandar: A novel multi-epitope peptide vaccine against cancer: an in silico approach (2014)
  7. Greco, Gianluigi; Terracina, Giorgio: Frequency-based similarity for parameterized sequences: formal framework, algorithms, and applications (2013)
  8. Malliavin, Thérèse E.; Mucherino, Antonio; Nilges, Michael: Distance geometry in structural biology: new perspectives (2013)
  9. Yaseen, Ashraf; Li, Yaohang: Accelerating knowledge-based energy evaluation in protein structure modeling with graphics processing units (2012) ioport
  10. Di Luccio, Eric; Koehl, Patrice: A quality metric for homology modeling: the H-factor (2011) ioport
  11. Pieper, Ursula; Webb, Benjamin M.; Barkan, David T.; Schneidman-Duhovny, Dina; Schlessinger, Avner; Braberg, Hannes; Yang, Zheng; Meng, Elaine C.; Pettersen, Eric F.; Huang, Conrad C.; Datta, Ruchira S.; Sampathkumar, Parthasarathy; Madhusudhan, Mallur S.; Sjölander, Kimmen; Ferrin, Thomas E.; Burley, Stephen K.; Sali, Andrej: Modbase, a database of annotated comparative protein structure models, and associated resources (2011) ioport
  12. Capriotti, Emidio; Martí-Renom, Marc A.: Quantifying the relationship between sequence and three-dimensional structure conservation in RNA (2010) ioport
  13. Duarte, Jose M.; Sathyapriya, Rajagopal; Stehr, Henning; Filippis, Ioannis; Lappe, Michael: Optimal contact definition for reconstruction of contact maps (2010) ioport
  14. Kushwaha, Sandeep K.; Shakya, Madhvi: Protein interaction network analysis -- approach for potential drug target identification in \textitMycobacteriumtuberculosis (2010)
  15. Rakshit, Sourav; Ananthasuresh, G. K.: A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization (2010)
  16. Benros, Cristina; de Brevern, Alexandre G.; Hazout, Serge: Analyzing the sequence-structure relationship of a library of local structural prototypes (2009)
  17. Pieper, Ursula; Eswar, Narayanan; Webb, Ben M.; Eramian, David; Kelly, Libusha; Barkan, David T.; Carter, Hannah; Mankoo, Parminder; Karchin, Rachel; Martí-Renom, Marc A.; Davis, Fred P.; Sali, Andrej: MODBASE, a database of annotated comparative protein structure models and associated resources (2009) ioport
  18. Ramana, Jayashree; Gupta, Dinesh: Lipocalinpred: a SVM-based method for prediction of lipocalins (2009) ioport
  19. Rangwala, Huzefa; Kauffman, Christopher; Karypis, George: \textitsvmprat: SVM-based protein residue annotation toolkit (2009) ioport
  20. Burke, David F.; Worth, Catherine L.; Priego, Eva-Maria; Cheng, Tammy; Smink, Luc J.; Todd, John A.; Blundell, Tom L.: Genome bioinformatic analysis of nonsynonymous SNPs (2007) ioport

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