{"id":352,"date":"2019-07-12T17:11:02","date_gmt":"2019-07-12T17:11:02","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/mgltools\/?page_id=352"},"modified":"2019-07-12T17:53:07","modified_gmt":"2019-07-12T17:53:07","slug":"doc-156-predefined-sets","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/mgltools\/doc-156-predefined-sets\/","title":{"rendered":"doc 156 predefined sets"},"content":{"rendered":"

Pmv predefined sets:<\/h2>\n

Residues:<\/p>\n

\u2018water\u2019<\/strong> =<\/p>\n

\u2018ions\u2019<\/strong> =<\/p>\n

\u2018DNA\u2019<\/strong> =<\/p>\n

\u2018RNA\u2019<\/strong> =<\/p>\n

\u2018ligand\u2019<\/strong> =<\/p>\n

‘acidic’<\/strong> = asp, glu<\/p>\n

‘acyclic’<\/strong> = ala, arg, asn, asp, cys, glu, gln, gly, ile, leu. lys, met, ser, thr, val<\/p>\n

‘aliphatic’<\/strong> = ala, gly, ile, leu, val<\/p>\n

\u2018aromatic’<\/strong> = his, phe, trp, tyr<\/p>\n

‘basic’<\/strong> = arg, his, lys<\/p>\n

‘buried’<\/strong> = ala, cys, ile, leu, met, phe, trp, val<\/p>\n

‘charged’<\/strong> = arg, asp, glu, his, lys<\/p>\n

‘cyclic\u2019<\/strong> = his, phe, pro, trp, tyr<\/p>\n

‘hydrophobic’<\/strong> = ala, gly, ile, leu, met, phe, pro, trp, tyr, val<\/p>\n

‘large’<\/strong> = arg, glu, gln, his, ile, leu, lys, met, phe, trp, tyr<\/p>\n

‘medium’<\/strong> = asn, asp, cys, pro, thr, val<\/p>\n

‘negative’<\/strong> = asp, glu<\/p>\n

‘neutral’<\/strong> = ala, asn, cys, gln, gly, his, ile, leu, met, phe, pro, ser, thr, trp, tyr, val<\/p>\n

‘polar’<\/strong> = arg, asn, asp, cys, glu, sln, his, lys, ser, thr<\/p>\n

‘positive’<\/strong> = arg, his, lys<\/p>\n

‘small’<\/strong> = ala, gly, ser<\/p>\n

‘surface’<\/strong> = arg, asn, asp, glu, gln, gly, his, lys, pro, ser, thr, tyr<\/p>\n

Atom Sets:<\/h3>\n

‘backbone’<\/strong> = C, CA, N, O<\/p>\n

‘backbone+h’<\/strong> = C, CA, N, O, HN, HN1, HN2<\/p>\n

‘sidechain’<\/strong> = SG, SD, CB, CG, CD, CD1, CD2, CE, CE1, CE2,<\/p>\n

CE3, CG1, CG2, CZ, CZ2, CZ3, CH2, ND1, ND2,<\/p>\n

NE, NE1, NE2, NH1, NH2, NZ, OD1, OD2,<\/p>\n

OG, OG1, OE1, OE2, OH, HD1, HE1, HE2,<\/p>\n

HE,HE21, HE22, HH23, HH11, HH12, HG,<\/p>\n

HG1, HH21, HD22, HD21, HZ1, HZ2, HZ3, HH<\/p>\n

One Character Residue Names:<\/h3>\n

ALA=A, ARG=R, ASN=N, ASP=D, ASX=B, CYS=C,<\/p>\n

GLU=E, GLN=Q, GLX=Z, GLY=G, HIS=H, ILE=I, LEU=L,<\/p>\n

LYS=K, MET=M, PHE=F, PRO=P, SER=S, THR=T, TRP=W<\/p>\n

TYR=Y, VAL=V, XAA=X, SEL=U<\/p>\n

#from www.ensembl.org\/Docs\/Pdoc\/bioperllive\/Bio\/SeqUtils.htm<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

Pmv predefined sets: Residues: \u2018water\u2019 = \u2018ions\u2019 = \u2018DNA\u2019 = […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-352","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/pages\/352","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/comments?post=352"}],"version-history":[{"count":3,"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/pages\/352\/revisions"}],"predecessor-version":[{"id":434,"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/pages\/352\/revisions\/434"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/mgltools\/wp-json\/wp\/v2\/media?parent=352"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}