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Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure has been solved.

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  • Modeller (it)
  • MODELLER (en)
  • MODELLER (ja)
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  • MODELLER（モデラー）は、タンパク質三次構造ならびに（稀にではあるが）四次構造のを構築するために使われるコンピュータプログラムである。MODELLERには「空間的制約の充足」として知られる (NMR) から着想を得た技術が実装されている。この技術では、幾何学的基準のセットがタンパク質内のそれぞれの原子の位置の確率密度関数を作るために使用される。この手法はモデリングする標的アミノ酸配列（シーケンス）と構造が解かれているテンプレート（鋳型）タンパク質との間のシーケンスアラインメントに頼っている。 このプログラムは、相同なタンパク質間でもしばしば高度に可変であるためホモロジーモデリングによる予測が困難なタンパク質のループ領域ののための限られた機能も取り込んでいる。 MODELLERはもとはカリフォルニア大学サンフランシスコ校のによって書かれ、現在もメンテナンスが行われている。学術的用途には無償で利用可能であるが、グラフィカルユーザインタフェース・商用版がによって配布されている。EasyModellerと呼ばれるMODELLERの無料GUIはインド・ハイデラバード大学のKuntal Kumar Bhusanによって開発された。また、にもMODELLERの単純なインターフェースが含まれている。JAVAベースのGUIであるSWIFT MODELLERも無料で配布されている。 (ja)
  • Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure has been solved. (en)
  • Modeller è un programma per computer utilizzato nella produzione di modelli di omologia sia di strutture terziarie che di strutture quaternarie (anche se quest'ultimo caso è più raro) di proteine . Essa attua una tecnica ispirata alla risonanza magnetica nucleare, nota come satisfaction of spatial restraints, mediante la quale un insieme di criteri geometrici vengono utilizzati per creare una funzione di densità di probabilità per il calcolo della posizione di ciascun atomo nella proteina. Il metodo si basa su una sequenza di input di allineamento (formato *.ali del file) tra la sequenza amminoacidica che deve essere modellata e il modello di proteina la cui struttura è stata risolta. (it)
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  • Modeller (en)
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  • Modeller (en)
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  • homology modeling of proteins (en)
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  • English (en)
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  • Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure has been solved. The program also incorporates limited functions for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous proteins and thus difficult to predict by homology modeling. Modeller was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco. It runs on the operating systems Unix, Linux, macOS, and Windows. It is freeware for academic use. Graphical user interfaces (GUIs) and commercial versions are distributed by Accelrys. The ModWeb comparative protein structure modeling webserver is based on Modeller and other tools for automatic protein structure modeling, with an option to deposit the resulting models into ModBase. Due to Modeller's popularity, several third party GUIs for MODELLER are available: * EasyModeller is freeware and is one of the earliest third party GUIs for Modeller. Recent version (EasyModeller 4.0) supports Linux and Windows operating system. * UCSF Chimera has a simple interface to Modeller. * PyMod is a free and open-source plugin for PyMOL and has a comprehensive interface for Modeller. It supports Linux, Windows and macOS. * MaxMod is a standalone GUI for MODELLER on Windows. (en)
  • MODELLER（モデラー）は、タンパク質三次構造ならびに（稀にではあるが）四次構造のを構築するために使われるコンピュータプログラムである。MODELLERには「空間的制約の充足」として知られる (NMR) から着想を得た技術が実装されている。この技術では、幾何学的基準のセットがタンパク質内のそれぞれの原子の位置の確率密度関数を作るために使用される。この手法はモデリングする標的アミノ酸配列（シーケンス）と構造が解かれているテンプレート（鋳型）タンパク質との間のシーケンスアラインメントに頼っている。 このプログラムは、相同なタンパク質間でもしばしば高度に可変であるためホモロジーモデリングによる予測が困難なタンパク質のループ領域ののための限られた機能も取り込んでいる。 MODELLERはもとはカリフォルニア大学サンフランシスコ校のによって書かれ、現在もメンテナンスが行われている。学術的用途には無償で利用可能であるが、グラフィカルユーザインタフェース・商用版がによって配布されている。EasyModellerと呼ばれるMODELLERの無料GUIはインド・ハイデラバード大学のKuntal Kumar Bhusanによって開発された。また、にもMODELLERの単純なインターフェースが含まれている。JAVAベースのGUIであるSWIFT MODELLERも無料で配布されている。 (ja)
  • Modeller è un programma per computer utilizzato nella produzione di modelli di omologia sia di strutture terziarie che di strutture quaternarie (anche se quest'ultimo caso è più raro) di proteine . Essa attua una tecnica ispirata alla risonanza magnetica nucleare, nota come satisfaction of spatial restraints, mediante la quale un insieme di criteri geometrici vengono utilizzati per creare una funzione di densità di probabilità per il calcolo della posizione di ciascun atomo nella proteina. Il metodo si basa su una sequenza di input di allineamento (formato *.ali del file) tra la sequenza amminoacidica che deve essere modellata e il modello di proteina la cui struttura è stata risolta. Il programma include anche una funzionalità limitata per la predizione della struttura delle regioni loop di proteine tramite il metodo Ab initio, anche se i loop sono spesso molto variabili anche tra proteine omologhe, e quindi hanno una struttura difficile da prevedere mediante modellazione per omologia. Modeller originariamente era stato scritto ed è attualmente gestito da Andrej Sali presso l'Università di California, San Francisco. Anche se è disponibile gratuitamente per uso accademico, l'interfaccia utente grafica s e le versioni commerciali sono distribuiti da Accelrys. Un GUI liberamente disponibile per Modeller chiamato EasyModeller è stato sviluppato da Kuntal Kumar Bhusan presso l'Università di Hyderabad, in India. Una nuova versione di EasyModeller (EasyModeller 2.0) è stato recentemente pubblicato e disponibile per il download gratuito. (it)
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