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A general introduction to structure prediction by two of the main developers of homology (Sali) and ab-initio (Baker) modeling. Baker, D; Sali, A (2001). "Protein structure prediction and structural genomics". Science 294 (5540): 93–96
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a more recent review of Comparative modeling that includes an updated list of online resources for structural modeling. Fiser A. (2017) Comparative Protein Structure Modelling. In: J. Rigden D. (eds) From Protein Structure to Function with Bioinformatics. Springer, Dordrecht
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Comparative Modeling (Homogloy modeling vs Threading)
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Seminal paper Sander,C. and Schneider,R. (1991) Proteins, 9, 56-68
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How high must the homology be for structure prediction to be reliable? Rost, B Twilight zone of protein sequence alignments, Protein Engineering, Design and Selection, Volume 12, Issue 2, 1 February 1999, Pages 85–94
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role in biologics/antibody modeling
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The papers describing the algorithms implemented in Prime (Honig, Shaw, Friesner). Jacobson, MP et al. "A Hierarchical Approach to All-Atom Protein Loop Prediction," Proteins 2004, 55, 351-367;
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SCWRL4 (Dunbrack Lab Fox Chase Cancer Center) Krivov, (2009), Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77: 778–795.
Virtual Ligand Screening Against Comparative Protein Structure Models Computational Drug Discovery and Design: pp 105-126