Pieper U, Eswar N, Davis F, Braberg H, Madhusudhan M, Rossi A, Marti-Renom M, Karchin R, Webb B, Eramian D, Shen M, Kelly L, Melo F. & Sali A. (2006) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research 34:D291-5

Karplus K, Karchin R, Shackelford G. & Hughey, R. (2005) Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics 21(22):4107-15

Karchin R, Diekhans M, Kelly L, Thomas D, Pieper U, Eswar N, Haussler D & Sali A (2005) LS-SNP: large-scale annotation of coding non-synonynous SNPs based on multiple information sources. Bioinformatics 21(12):2814-20

Karchin R, Kelly L & Sali A (2005) Improving functional annotation of non-synonymous SNPs with information theory. Pacific Symposium on Biocomputing 10:397-408

Karchin R, Cline M & Karplus K (2004) Evaluation of local structure alphabets based on residue burial. Proteins 55(3):508-18

Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins. 2003;53 Suppl 6:491-6. doi: 10.1002/prot.10540. PMID: 14579338.

Karchin R, Cline M, Mandel-Gutfreund Y. & Karplus K. (2003) Hidden Markov models that use predicted local structure for fold recognition: alphabets of protein backbone geometry. Proteins 51(4):504-514

Karchin R, Karplus K & Haussler, D (2002) Classifying G-Protein Coupled Receptors with Support Vector Machines. Bioinformatics 18(1):147-159

Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M Grate, L Casper, J & Hughey R. (2001) What is the value added by human intervention in protein structure prediction? Proteins 45(S5):86-91

Karchin R & Hughey R (1998) Weighting Hidden Markov Models for Maximum Discrimination. Bioinformatics 14(9):772-82