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Flexible protein folding by ant colony optimization [PDF]
, 2008 Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the ...
Hu, X., Li, Y., Zhang, J.
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ClusterEmbed: Lightweight Protein Structure Prediction on PCs [PDF]
BIO Web of ConferencesBiological sequence design seeks to generate novel sequences, such as proteins, with optimized functional properties, a task complicated by vast combinatorial spaces and complex sequence-function relationships.
Yuan Chuxin
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Domain discovery method for topological profile searches in protein structures [PDF]
, 2004 We describe a method for automated domain discovery for topological profile searches in protein structures. The method is used in a system TOPStructure for fast prediction of CATH classification for protein structures (given as PDB files).
Gilbert, D, Torrance, G, Viksna, J
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On the optimal contact potential of proteins
, 2007 We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies.
Akira R. Kinjo +32 more
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Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins. [PDF]
, 2013 Of the membrane proteins of known structure, we found that a remarkable 67% of the water soluble domains are structurally similar to water soluble proteins of known structure. Moreover, 41% of known water soluble protein structures share a domain with an
Bowie, James U +3 more
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Frontiers in Molecular Biosciences, 2021 Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design.
Farhan Quadir +3 more
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Structure prediction of alternative protein conformations
Nature CommunicationsProteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB.
Patrick Bryant, Frank Noé
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LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction
Frontiers in Molecular Biosciences, 2021 Protein-protein docking is a useful tool for modeling the structures of protein complexes that have yet to be experimentally determined. Understanding the structures of protein complexes is a key component for formulating hypotheses in biophysics ...
Charles Christoffer +4 more
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Improving protein fold recognition using the amalgamation of evolutionary-based and structural-based information [PDF]
, 2014 Deciphering three dimensional structure of a protein sequence is a challenging task in biological science. Protein fold recognition and protein secondary structure prediction are transitional steps in identifying the three dimensional structure of a ...
Dehzangi, A. +3 more
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Local protein structure prediction using discriminative models
BMC Bioinformatics, 2006 Background In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in fold recognition incorporation of local structure ...
Lengauer Thomas +2 more
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