Results 201 to 210 of about 87,514 (244)
Some of the next articles are maybe not open access.
Ensemble Docking from Homology Models
Journal of Chemical Theory and Computation, 2010We present here a systematic exploration of the quality of protein structures derived from homology modeling when used as templates for high-throughput docking. It is found that structures derived from homology modeling are often similar in quality for docking purposes than real crystal structures, even in cases where the template used to create the ...
Eva Maria, Novoa +3 more
openaire +2 more sources
2009
Over 1,000 sequences likely to encode G protein-coupled receptors (GPCRs) are currently available in publicly accessible and proprietary databases and this number may grow with the refinement of a number of different genomes. However, despite recent efforts in the crystallization of these proteins, homology modeling approaches are becoming widely used ...
John, Simms +6 more
openaire +2 more sources
Over 1,000 sequences likely to encode G protein-coupled receptors (GPCRs) are currently available in publicly accessible and proprietary databases and this number may grow with the refinement of a number of different genomes. However, despite recent efforts in the crystallization of these proteins, homology modeling approaches are becoming widely used ...
John, Simms +6 more
openaire +2 more sources
Homology Modeling of Divergent Proteins
Journal of Molecular Biology, 1994A method is presented for homology modeling of proteins bearing weak sequence identity to proteins of known tertiary structure. To accommodate non-identical amino acids in the core region, the backbone of the structurally conserved core of the model protein is allowed to deviate from that of the template protein.
S, Sudarsanam, C J, March, S, Srinivasan
openaire +2 more sources
Homology Modeling of P2X Receptors
2019Since the X-ray structure of the zebra fish P2X4 receptor in the closed state was published in 2009 homology modeling has been used to generate structural models for P2X receptors. In this chapter, we outline how to use the MODELLER software to generate such structural models for P2X receptors whose structures have not been solved yet.
Anastasios, Stavrou +2 more
openaire +2 more sources
Probabilistic protein homology modeling
2014Searching sequence databases and building 3D models for proteins are important tasks for biologists. When the structure of a query protein is given, its function can be inferred. However, experimental methods for structure prediction are both expensive and time consuming.
openaire +2 more sources
Antibody modeling: Beyond homology
ImmunoMethods, 1992The immune system is capable of producing at least 109 different antibody specificities. There are currently about 800 variable-region sequences known, whereas there are only 16 deposited Fab structures. Thus, the rate of sequence acquisition far outstrips the rate of structure determination.
Jan Pedersen +3 more
openaire +1 more source
Homology Modeling of Protein Targets with MODELLER
2019Homology modeling is a computational approach to generate three-dimensional structures of protein targets when experimental data about similar proteins are available. Although experimental methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy successfully solved the structures of nearly 150,000 macromolecules, there is still
Gabriela, Bitencourt-Ferreira +1 more
openaire +2 more sources
Force Fields for Homology Modeling
2011Accurate all-atom energy functions are crucial for successful high-resolution protein structure prediction. In this chapter, we review both physics-based force fields and knowledge-based potentials used in protein modeling. Because it is important to calculate the energy as accurately as possible given the limitations imposed by sampling convergence ...
openaire +2 more sources
Modelling mutations and homologous proteins
Current Opinion in Biotechnology, 1995A protein sequence with at lease 40% identity to a known structure can now be modelled automatically, with an accuracy approaching that o fa low-resolution X-ray structure or a medium-resolution nuclear magnetic resonance structure. In general, these models have goods stereochemistry and an overall structural accuracy that is as high as the similarity ...
openaire +2 more sources
Splice variants: A homology modeling approach
Proteins: Structure, Function, and Bioinformatics, 2003AbstractSplice variants play an important role within the cell in both increasing the proteome diversity and in cellular function. Splice variants are also associated with disease states and may play a role in their etiology. Information about splice variants has, until now, mostly been derived from the primary transcript or through cellular studies ...
Nicholas, Furnham +2 more
openaire +2 more sources