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by Proteins Structure , Genetics Published , John Wiley , Marc Nadeau , Marc Nadeau

Citations

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70	Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry.” - Karchin, Cline - 2003 (Show Context) Citation Context ... mutual information describes how much the likelihood of observing b was influenced by the observation of a. The average mutual information is computed as follows: M�a, b� � �p�a, b�log a,b p�a, b� , =-=(1)-=- p�a�p�b� where p(a) and p(b), the probabilities of individual letters a and b, are estimated by the frequency with which they appear in the representative set of the FSSP alignments and their joint p...
69	Predicting protein structure using hidden Markov models - Karplus, Sjolander, et al. - 1997
69	What is the value added by human intervention in protein structure prediction - Karplus, Karchin, et al. - 2001
63	Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations - Betancourt, Thirumalai - 1999
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11	Ramensky V, Koch I, Lathe W III, Kondrashov AS, Bork P. Prediction of deleterious human alleles. Hum Mol Genet 2001;10: 591–7 - Sunyaev (Show Context) Citation Context ...re, but is scaled to a related quantity called s(i), which is 1 for 0 shifts and approaches �ε (ε is typically set at 0.2) for large shifts: �� 1 � ε � � ε if shift(i) isdefined s�i� 1 � �shift�i�� . =-=(4)-=- 0 otherwise The scaling of shift(i) to s(i) avoids having a mean shift-error term dominated by large positive or negative shifts. With ε set at 0.2, shift-score ranges from �0.2 (worst) to 1.0 (best)...
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8	Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit - AG, DE, et al. - 2001
7	Evaluating local structure alphabets for protein structure prediction - Karchin - 2003
7	The bottom line for prediction of residue solvent accessibility - CJ, Barlow - 1999
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6	An alternative view of protein fold space. Proteins 2000;38:247–260 - IN, PE
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5	Potential of fumarate reductase as a novel therapeutic target in Helicobacter pylori infection. Expert Opin Ther Targets 6 - Ge - 2002
4	Surprising similarities in the structure comparison - Gilbrat, Madej, et al. - 1996 (Show Context) Citation Context ...ts STR 13 0.103 1.107 1.009 STRIDE 6 0.088 0.904 0.863 STRIDE-EHL 3 0.075 0.861 0.736 ANG 10 0.228 0.678 0.736 TCO 4 0.095 0.623 0.577 identity (3% to 24%) but significant structural similarity (VAST =-=[38]-=- p-value �0.0001, Yale 39 RMSD � 4.0 Å, and a DALI 26 Z-score � 7.0). Datasets are available at http://www.soe.ucsc.edu/ research/compbio/2thmm. RESULTS Conservation and Predictability For a burial me...
4	Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables - SM, KM - 1993
3	Investigation of non-pairwise protein structure score functions using sets of decoy structures - Barrett - 2001
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2	Haussler D. Information-theoretic dissection of pairwise contact potentials. Proteins 2002;49:7–14 - RG
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