PRIMO: An Interactive Homology Modeling Pipeline. [PDF]
PLoS ONE, 2016 The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process.
Rowan Hatherley +3 more
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Homology modeling and mutation prediction of ACE2 from COVID-19 [PDF]
Pharmaciana, 2021 SARS-CoV-2 has become a pandemic in the world. The virus binds to the Angiotensin-Converting Enzyme 2 (ACE2) receptor, which is found in epithelial cells such as in the lungs, to generate the pathology of COVID-19.
Purnawan Pontana Putra +5 more
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Homology modeling in the time of collective and artificial intelligence
Computational and Structural Biotechnology Journal, 2020 Homology modeling is a method for building protein 3D structures using protein primary sequence and utilizing prior knowledge gained from structural similarities with other proteins.
Tareq Hameduh +3 more
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Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation [PDF]
PeerJ, 2021 GPCRs (G-protein coupled receptors) are the largest family of drug targets and share a conserved structure. Binding sites are unknown for many important GPCR ligands due to the difficulties of GPCR recombinant expression, biochemistry, and ...
Ashley Ryan Vidad +2 more
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Sequence alignment generation using intermediate sequence search for homology modeling
Computational and Structural Biotechnology Journal, 2020 Protein tertiary structure is important information in various areas of biological research, however, the experimental cost associated with structure determination is high, and computational prediction methods have been developed to facilitate a more ...
Shuichiro Makigaki, Takashi Ishida
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Homology in Electromagnetic Boundary Value Problems
Boundary Value Problems, 2010 We discuss how homology computation can be exploited in computational electromagnetism. We represent various cellular mesh reduction techniques, which enable the computation of generators of homology spaces in an acceptable time. Furthermore, we show how
Matti Pellikka +2 more
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Ten quick tips for homology modeling of high-resolution protein 3D structures.
PLoS Computational Biology, 2020 The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using ...
Yazan Haddad, Vojtech Adam, Zbynek Heger
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FINDSITE: a threading-based approach to ligand homology modeling. [PDF]
PLoS Computational Biology, 2009 Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new methodologies is required.
Michal Brylinski, Jeffrey Skolnick
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Accurate protein stability predictions from homology models
Computational and Structural Biotechnology Journal, 2023 Calculating changes in protein stability (ΔΔG) has been shown to be central for predicting the consequences of single amino acid substitutions in protein engineering as well as interpretation of genomic variants for disease risk.
Audrone Valanciute +5 more
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Quality Assessment of Selected Protein Structures Derived from Homology Modeling and AlphaFold
Pharmaceuticals, 2023 With technology advancing, many prediction algorithms have been developed to facilitate the modeling of inherently dynamic and flexible macromolecules such as proteins.
Furkan Ayberk Binbay +3 more
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