ECOD: an evolutionary classification of protein domains
Cheng, Hua, Schaeffer, R. Dustin, Liao, Yuxing, Kinch, Lisa N., Pei, Jimin, Shi, Shuoyong, Kim, Bong-Hyun, Grishin, Nick V.·2014·PLoS Computational Biology
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- ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known StructureAya Narunsky, Sergey Nepomnyachiy, Haim Ashkenazy, Rachel Kolodny, Nir Ben‐Tal · 2015 · Structure
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