


PFRMAT FRV1
REMARK ========================================================================
REMARK Threading results for the target T0021, compared against a fold library,
REMARK which contains only the globin fold currently, but will be extended to
REMARK contain more folds.  
REMARK 
REMARK Fold definition: cores defined by LPFC (Library of Protein Family
REMARK      Core Structures, http://www-smi.stanford.edu/projects/helix/LPFC/)
REMARK Fitness function: After a target sequence is aligned to a fold, for each
REMARK      Cb postion, the environment around is represented by the 
REMARK      the distribution of multi-level physico-chemical properties up to
REMARK      10 Angstrom.  The environment is then statistically compared to
REMARK      the corresponding environments in a set of nonhomologous proteins
REMARK      that have the fold (sites), and to randomly shuffled environments
REMARK      (nonsites).  For each Cb position, a fitness score is given which
REMARK      measures how well the environment fits the sites instead of the
REMARK      nonsites (Wei & Altman, in preparation).  The overall fitness 
REMARK      score is the sum over all Cb positions.
REMARK Search for optimal alignment: For each fold, multiple alignment of
REMARK      proteins known to have the fold provides a distribution of observed
REMARK      gap positions and a distribution of gap lengths. The distritutions
REMARK      are sampled to generate gap positions and lengths for the target 
REMARK      sequences.
REMARK Ranking of compatibility score:  Sequence/fold compatibility is ranked
REMARK      by Z-scores.  For each sequence/fold pair, a Z-score is computed
REMARK      from the fitness score for optimal alignment, which is compared to 
REMARK      distribution of fitness scores for optimally aligning shuffled
REMARK      sequences of proteins known to have the fold.
REMARK ========================================================================
AUTHOR 2286-2612-8205 Jeffrey Chang, Stanford University
AUTHOR 2286-2612-8205 Section on Medical Informatics
AUTHOR 1244-8530-3384 Liping Wei, Stanford University
AUTHOR 1244-8530-3384 Section on Medical Informatics
AUTHOR Russ Altman, Stanford University
AUTHOR Section on Medical Informatics
REMARK ========================================================================
SEQRES T0021 GAKEPDPDKLKKAIVQVEHDERPARLILNRRPPAEGYAWLKYEDDGQEFEANLADVKLVA
SEQRES T0021 LIEG
REMARK ========================================================================
TSCORE T0021 0  1.0     NONE - 0
TSCORE T0021 0  0.0     1HLB - 1
REMARK ========================================================================
STRSUB 1HLB - 1  13   15
STRSUB 1HLB - 1  17   28
STRSUB 1HLB - 1  34   51
STRSUB 1HLB - 1  69   88
STRSUB 1HLB - 1  92  126
STRSUB 1HLB - 1 137  152
REMARK ========================================================================



