PIKO standart (project)
Introduction.
METHOD Method description
METHOD The strong correlation dependence of spatial structure
METHOD of the protein from its nucleotide sequence was
METHOD theoretically predicted by physical modelling,
METHOD experimentally discovered and statistically confirmed.
METHOD In the process of biosynthesis the third nucleotide of
METHOD the codon controls the orientation of the amino acid
METHOD forming the concrete spatial isomer that is the
METHOD conformation of the protein molecule cutting off
METHOD competition ways of the forming of 2D and 3D structures.
METHOD On this base the computer program Pikotechnology for
METHOD the prediction of 2D structure of the protins on their
METHOD nucleotide sequence was created.
Composition genetic code table (1992)
Samples:
Origin size:
img-fotki.yandex.ru/get/5700/nanoworld.2...d1_768200e6_orig.png
Origin size:
img-fotki.yandex.ru/get/4402/nanoworld.2...02_8b0a1fc2_orig.png
Origin size:
img-fotki.yandex.ru/get/5106/nanoworld.2...08_9fa5c119_orig.gif
Origin size:
img-fotki.yandex.ru/get/4714/126580004.3...fd_af7c9696_orig.gif
Collagen, 3D structure
Origin size:
img-fotki.yandex.ru/get/4525/126580004.3...50_31b552b6_orig.gif
Collagen, 4-structure, Helix
Origin size:
img-fotki.yandex.ru/get/3008/126580004.3...ee_51f54771_orig.png
Collagen, 4-structure, Helix
Origin size:
img-fotki.yandex.ru/get/4426/126580004.3...02_4d48f4b5_orig.gif
Collagen, 4-structure, piko-precision
Origin size:
img-fotki.yandex.ru/get/4525/126580004.3...48_451d0c8f_orig.gif
Insulin, 3D-structure
Origin size:
img-fotki.yandex.ru/get/5706/nanoworld20...8a_18732968_orig.gif
Insulin, 3D-structure
Insulin, 2D-structure (PIKO-2D standart (project))
compositional code:
1,1,4,1,1,4,1,4,4,1,4,1,4,1,4,1,1,1,4,1,1,4,1,1,4,4,3,3,4,1,4,1,1,1,1,1,4,1,1,3,1,1,1,1,1,4,1,1,1,4,1
Kushelev's script for 3DS Max:
angx=#(-24,180,60,-45,-45); angy=#(-10.89167,83,0,15,15); angz=#(92,120,60,110,110)
dx=#(2,1.5,1.6,2,2); dy=#(0.6,1,0.8,1,0.6); dz=#(-0.45,0,-0.6,-0.15,-0.45)
kk=#(1,1,4,1,1,4,1,4,4,1,4,1,4,1,4,1,1,1,4,1,1,4,1,1,4,4,3,3,4,1,4,1,1,1,1,1,4,1,1,3,1,1,1,1,1,4,1,1,1,4,1,1,1,1,1,1)
peptide=box length:1 width:1 height:1 position:[0,0,-.5] wirecolor:[250,250,250]; Converttomesh peptide
for k = 1 to 56 do(
element = Hedra family:1 scalep:100 scaleq:100 scaler:100 radius:1 pos:[0,0,0] p:0.4; Converttomesh element
attach peptide element; peptide.pivot = [0,0,0]; move peptide [dx[kk[k]],dy[kk[k]],dz[kk[k]]]
rotate peptide angx[kk[k]] [1,0,0]; rotate peptide angy[kk[k]] [0,1,0]; rotate peptide angz[kk[k]] [0,0,1])
Origin size:
nanoworld88.narod.ru/data/263_files/0_af548_451d0c8f_orig.gif
Kushelev's script - top model
Origin size:
img-fotki.yandex.ru/get/5414/126580004.3...20_2c87f90a_orig.gif
Insulin, 3D-structure, piko-precision (PIKO-3D standart (project))
Savin-Kushelev's script result
Savin-Kushelev's script for 3DS Max (Light):
nanoworld.narod.ru/EMBLReader023L_20101113.txt
Details:
nanoworld88.narod.ru/data/212.htm
Input data:
ID OCINSAA standard; RNA; MAM; 250 BP.
XX
AC M61153;
XX
DT 12-APR-1991 (Rel. 28, Created)
DT 15-APR-1994 (Rel. 39, Last updated, Version 2)
XX
DE Oryctolagus cuniculus insulin mRNA, partial cds.
XX
KW insulin.
XX
OS Oryctolagus cuniculus (rabbit)
OC Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Mammalia;
OC Theria; Eutheria; Lagomorpha; Leporidae.
XX
RN [1]
RP 1-250
RA Giddings S.J., Carnaghi L., Devaskar S.;
RT Nucleotide sequence of a cDNA encoding rabbit preproinsulin;
RL Unpublished.
XX
CC NCBI gi: 165444
XX
FH Key Location/Qualifiers
FH
FT source 1..250
FT /organism=Oryctolagus cuniculus
FT CDS 1..168
FT /note=NCBI gi: 470321
FT /product=insulin
FT /codon_start=1
XX
SQ Sequence 250 BP; 36 A; 105 C; 78 G; 31 T; 0 other;
cgcgaggtgg aggagctgca ggtggggcag gcggagctgg gcgggggccc cggcgcgggc
ggcctgcagc cctcggcgct ttatctggcc ctgcagaagc gcggcatcgt ggagcagtgt
tgcaccagca tctgctcgct ctaccagctg gagaactact gcaactaggg gtgcccccca
cccacccctg cccgcgcccc ccacgccccc cgccctcgcc cccacccaat aaacccctcc
acgcgccccc
//
Output data:
PFRMAT TS
TARGET T00xx
AUTHOR 4236-1297-6301
REMARK Nanoworld Laboratory
REMARK
nanoworld.narod.ru
REMARK Predictor remarks. See DEMO:
REMARK
nanoworld88.narod.ru/data/270.htm
REMARK
REMARK Target sequence (56 acids)
REMARK REVEELQVGQAELGGGPGAGGLQPSALYLALQKRGIVEQCCTSICSLYQLENYCN*
REMARK
METHOD Method description
METHOD The strong correlation dependence of spatial structure
METHOD of the protein from its nucleotide sequence was
METHOD theoretically predicted by physical modelling,
METHOD experimentally discovered and statistically confirmed.
METHOD In the process of biosynthesis the third nucleotide of
METHOD the codon controls the orientation of the amino acid
METHOD forming the concrete spatial isomer that is the
METHOD conformation of the protein molecule cutting off
METHOD competition ways of the forming of 2D and 3D structures.
METHOD On this base the computer program Pikotechnology for
METHOD the prediction of 2D structure of the protins on their
METHOD nucleotide sequence was created.
MODEL 1
PARENT N/A 1
ATOM 1 N ARG A 1 10.504 6.874 4.374 1.00 0.50 A
ATOM 2 CA ARG A 1 9.740 6.273 4.413 1.00 0.50 A
ATOM 3 C ARG A 1 9.285 5.939 3.569 1.00 0.50 A
Details:
nanoworld.org.ru/topic/199/page/28/
Origin size:
img-fotki.yandex.ru/get/5414/126580004.3...22_33995f57_orig.gif
***
1. Sokolik V.V. Algorithm of protein structural template decoding according to its determined nucleotide sequence // Fist International Conference “Fundamental Medicine: From Scalpel Toward Genome, Proteome and Lipidome” (April 25-28, 2011), Pax Grid Virtual Conferences, Kazan, Russia. – P. 117-119.
2. Sokolik V.V. Protein is coded in genome and synthesized in ribosomes as a structural template of a rotameric version sequence of peptide bound configuration // The International Moscow Conference on Computational Molecular Biology, МССМВ-11 (July 21-24, 2011), Moscow, Russia. – P. 347-348.
Отредактировано kushelev (2012-01-11 16:48:07)