def TMclstr(fp): import scipy.cluster.hierarchy as sch import scipy.spatial.distance as ssd #read represent id list replist=read_clstr_represent(fp) lenlist=len(replist) #read TMscore matrix vec=[] f=file('TM.txt') for i in range(0,lenlist): for j in range(i+1,lenlist): a = f.readline().strip().split() t=1-float(a[2]) vec.append(t) f.close() #Clustering linkage_matrix=sch.linkage(ssd.squareform(vec)) #print linkage_matrix ind=sch.fcluster(linkage_matrix,0.95) inx=range(0,lenlist) data=zip(ind,inx) data.sort() for i,j in data: print replist[j],i

# Algorithm

# run matlab m function

enter the dir where you put the m file that includes m function. and just use the m function.

# RASP tools v1.0 available

RASP tools is a tool package for protein side-chain assessment. It is also available at the RASP v1.80 site: https://sourceforge.net/projects/raspv180/ With the 3 tools: RASPsym, RASPchi and RASPrmsd, we can: 1. flip the symmetric side-chains to the same side; 2. calculate protein side-chain dihedral angles; 3. calculate side-chain RMSD or PDB rmsd. The RASP logo … Continue reading RASP tools v1.0 available

# RASP version 1.80

RASP program for protein side-chain structure prediction has been updated Jan 7th 2013. The new version is 1.80 and available here: https://sourceforge.net/projects/raspv180/ Happy new year, Everyone! Have fun with the updated program.

# android app for threading

jFR apk client for android http://sourceforge.net/projects/apkclientforjfr/ jFR is a threading program for protein structure prediction.

# pseudocode for Dead-end Elimination

for each position i for each rotamer s at i for each candidate rotamer r at i X←E(is)-E(ir) for all rotamers t at position j, j¹i Y←min[E(is,jt)-E(ir,jt)] end X←X+Y if(X>0) exclude is and return end end end