Predicting protein structure using only sequence information
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Updated: Oct 18, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
K Karplus1, C Barrett, M Cline
1John Baskin School of Engineering, University of California, Santa Cruz 95064, USA. karplus@cse.ucsc.edu
Abstract:
This paper presents results of blind predictions submitted to the CASP3 protein structure prediction experiment. We made predictions using the SAM-T98 method, an iterative hidden Markov model-based method for constructing protein family profiles. The method is purely sequence-based, using no structural information, and yet was able to predict structures as well as all but five of the structure-based methods in CASP3.
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