Prediction of protein function from protein sequence and structure

By James C. Whisstock, Arthur M. Lesk. 2003

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In Molecular Biology

Citations in the corpus

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields (2015, neutral): “ first for CRF and then for DCNN. The gradient of the log-likelihood with respect to the parameters � and � is given by, 𝛻� �,� =[∑Å𝑖=1𝛿(�𝑖=�)𝛿(�𝑖+1=�)]−𝐸�𝑃𝑃(�|�,�,�,�)[∑ 𝛿(�𝑖=�)𝛿(�𝑖+1=�) Å 𝑖=1 ] (6) 𝛻� �,� =[∑Å𝛿(�𝑖=�)𝐻�(�,𝑖,�) 𝑖=1 ]−𝐸�𝑃𝑃(�|�,�,�,�)[∑ 𝛿(�𝑖=�)𝐻�(�,𝑖,�) Å 𝑖”
Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “3 Accurate protein structures are necessary as starting points for rational drug design, 4 protein engineering applications, 5 and to understand functional implications of mutations associated with genomic variations within populations.”
Protein function prediction via graph kernels (2005, background): “Exceptions are also numerous if similarity is measured by means other than structure (Whisstock and Lesk, 2003).”
Predicting protein function from sequence and structure (2007, unknown): “However, as the volume of data has increased, so too have the number and sophistication of computational methods for predicting functio”
The biological impact of mass-spectrometry-based proteomics (2007, background): “jpg" NDATA ITEM> ]> Of the many fascinating discoveries made by genome-sequencing projects, perhaps none is more provocative than the prediction that all prokaryotes and eukaryotes produce numerous proteins with uncharacterized or pleiotropic function”
Predicting protein function from sequence and structural data. (2005, background): “The more similar the sequence, the more similar the function is likely to be, although there are cases of proteins having 100% sequence identity yet performing different roles according to where they are expressed [1].”
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008, background): “Structural information can align the residues in this common core, even after the sequences have diverged too far for successful sequence-based alignment, because structural similarity is typically more evolutionarily conserved [5–7].”
Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations (2018, background): “Proteins have evolved over billions of years to form highly complex structures, which give rise to a diverse range of functions.(1,2) The atomistic details of their structure are of great importance to develop a deeper understanding of their function as well as to develop novel pharmaceutical strate”
Structure-based Systems Biology for Analyzing Off-target Binding (2011, background): “Tremendous efforts have been made in detecting global sequence and structure similar proteins to infer their functional relationship [30].”