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Q.No#2what is DNA Arrays, detail note on types and applications of microarray }{\b1
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chip or biochip)is a collection of microscopic spots attached to a solid surface.}
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\af0 \dbch \f0 \cf0 :DNA microarray to measure the expression level of the large
numbers of the genes simultaneously or to genotype multiple region of the genome.:}
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\f0 \cf0 Microarray used for cancer research,It provide assistance in pharmacology
approach to treat various diseases including oral lesions}{\fs21 \kerning2 \loch
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\aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch
\af0 {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0 It is used in analyzing
large amount of the sampe which have either been recorded previously or new
sample,it evenhelps to test the incidence of a particular marker in tumors.}
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0 \par }\pard \plain \qj
\li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0
\itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0
Types of Microarray:}{\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0 \par
}\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright
\lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0 DNA microarray is also known as gene
chip,DNA chip or biochip.It either measure DNA or uses DNA as part of its detection
system.There are four different types of DNA microarray.cDNA,Oligo DNA
microarrays,BAC microarrays and SNP microarrays.}{\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0
1)cDNA }{\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf0 \par }\pard
\plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright
\lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs24
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf1 \uc1 \u160 ?DNA\uc1 \u160 ?
synthesized from a single stranded RNA (e.G., messenger RNA (mRNA) or\uc1 \u160 ?
microRNA) template in a reaction catalyzed through the enzyme\uc1 \u160 ?opposite
transcriptase. CDNA is regularly used to clone\uc1 \u160 ?eukaryotic\uc1 \u160 ?
genes\uc1 \u160 ?in\uc1 \u160 ?prokaryotes.The time period\uc1 \u160 ?cDNA\uc1
\u160 ?is likewise used, generally in a\uc1 \u160 ?bioinformatics\uc1 \u160 ?
context, to refer to an mRNA transcript's sequence, expressed as DNA bases (GCAT)
in preference to RNA bases (GCAU).}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\cf1 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\b1 \fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf1 DNA Microarray}{\b1 \fs24
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \cf1 \par }\pard \plain \qj \li0 \ri0
\lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21
\kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs24 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \cf1 A DNA microarray (additionally generally referred to as DNA
chip or biochip) is a set of microscopic DNA spots connected to a stable floor.
Every DNA spot consists of picomoles (10}{\fs24 \kerning2 \dbch \af4 \hich \af4
\loch \f4 \cf1 \uc1 \u8722 ?}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\lang1033 \langnp1033 \cf1 12 moles) of a particular DNA collection, referred to as
probes (or reporters or oligos).}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf1 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0
\widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2
\dbch \af2 \hich \af0 \loch \af0 {\b1 \fs24 \kerning2 \loch \af0 \hich \af0
\dbch \f0 \lang1033 \langnp1033 \cf1 BAC Microarray;}{\b1 \fs24 \kerning2 \loch
\af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1 \par }\pard \plain \qj \li0
\ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0
\fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 A\uc1 \u160 ?BAC\uc1 \u160 ?clone
chip is a DNA\uc1 \u160 ?microarray\uc1 \u160 ?whose probe is a template amplified
by PCR. ...\uc1 \u160 ?BAC\uc1 \u160 ?is a vector that can clone a gene of 100-300
kb long. A\uc1 \u160 ?BACclone chip is used to analyze the number of genomic DNA
copies in such methods as the CGH array.}{\fs21 \kerning2 \loch \af0 \hich \af0
\dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0
\widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2
\dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0
\widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2
\dbch \af2 \hich \af0 \loch \af0 {\b1 \fs24 \kerning2 \loch \af0 \hich \af0
\dbch \f0 \lang1033 \langnp1033 \cf1 SNP MICROARRAY}{\b1 \fs24 \kerning2 \loch
\af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1 \par }\pard \plain \qj \li0
\ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0
\fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 In molecular biology,\uc1 \u160 ?
SNP array\uc1 \u160 ?is a type of DNAmicroarray\uc1 \u160 ?which is used to detect
polymorphisms within a population. A single nucleotide polymorphism (SNP), a
variation at a single site in DNA, is the most frequent type of variation in the
genome.}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\b1 \fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1
Question:no:3: }{\b1 \fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 (Q.2) detail note the problems occur during of peptide sequencing.
[5]}{\b1 \fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1
Messpectrometer has facilited in the sequencing of protein but there are some
problem . In that process,So when the mass spectrometer it break the small fragment
into a further small fragment then the problem is that despite having the small
fragment of some molecule that are attached in with the molecule removed. When the
small peptide or with the amino acid they are removed,then the mass that is
calculated through the mass spectrometer is diferent then the actual mass of
protein or peptide.actual protein or peptide protein have linear shape. Mass
spectrometer break the protein into small fragment of protein having N and C
terminal. If the protein}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf1 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf1 breaken from N terminal it creates small fragment also If it break
from c terminal . If the sequence break there is a problem in detecting the
sequencing of the protein by using spectrphotometer . If we break it into fragment
it may cause small part of proteinmay lose and resulting in fragment of lower
masses, for example}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf1 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf1 Amass spectrometer breaks a peptide p1 p2 \uc1 \u183 ? \uc1
\u183 ? \uc1 \u183 ? pn}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\lang1033 \langnp1033 \cf1 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0
\widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2
\dbch \af2 \hich \af0 \loch \af0 {\fs24 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf1 GPFNA }{\fs24 \kerning2 \loch
\af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1 \tab }{\fs24 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1 \tab }{\fs24
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1
GPFNA}{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033
\cf1 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich
\af0 \loch \af0 {\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf1 G, GP, GPF, GPFN PFNA, FNA, NA, A GPFNA into
GP and FNA , lose some small parts of GP and FNA, fragments of a lower mass}
{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs24 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1 GP
might lose a water (H2O), and the peptide FNA might lose an ammonia (NH3). Mass of
GP minus the mass of water (1 + 1 + 16 = 18 daltons) , and the mass of FNA minus
the mass of ammonia (1 + 1 + 1 + 14 = 17 daltons). Two different ion types.we know
peptide GP may lose water molecule , if water is release . The mass of CGPA will
reduce one similarly the peptide FNA may loss molecule of amonia, then the mass is
reduced. The resulting mess is detected by spectrometer will be equal to the mess
of GP the mess of water we can calculated the mean of GP and we can calculated the
mean of water.NH=17 , we have to remove 17 from this FNA ,peptide missing FNA NH3
and water two different ion type that can considerd in fragmenting,that may cause
problem in sequencing of the protein due to lowering mass.}{\fs24 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf1 \par }\pard \plain
\qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0
\rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\b1 \fs24
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 (Q no
5)Explain how computer algorithms can be used to predict the primary, secondary and
tertiary structures of proteins}{\b1 \fs24 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0
\widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2
\dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf0 ANS:A computer algorithms is well defined procedure
that allows a computer to solve a problems.}{\fs21 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0
\lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21
\kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Computer algorithm is used to find the
protein structer.different algorithm is used to find the different protein
structer. Such as}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\lang1033 \langnp1033 \cf0 Chou Fasman Algorithm - I}{\b1 \fs21 \kerning2 \loch
\af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0
\ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0
\fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Only a small number of combinations
of secondary structures are possible due to their individual properties.Such as 4
amino acids are needed to start an Alpha Helix and 5 amino acids for Beta
Sheet.Note that besides the alpha helix and beta sheets, LOOPS are an other
secondary structure}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 It is used to find the secondary structer of a protein which
include alpha helix,beta sheet, and loop,by using propensity table.}{\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard
\plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright
\lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Protein
Structure Database - PDB Online tools for predicting structures such as MODELLER
and iTASSER}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\lang1033 \langnp1033 \cf0 ITASSER:}{\b1 \fs21 \kerning2 \loch \af0 \hich \af0
\dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0
\widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2
\dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf0 I-TASSER (Iterative Threading ASSEmbly Refinement)
is a hierarchical approach to protein structure and function prediction.}{\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard
\plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright
\lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 I-TASSER: A
standalone I-TASSER package for protein 3D structure prediction and refinement.}
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
QUARK}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
is a computer algorithm for ab initio protein structure prediction and protein
peptide folding, }{\fs21 \kerning2 \dbch \af0 \hich \af0 \loch \f0 \lang1033
\langnp1033 \cf0 which is used to predict the 3d structer of protein.}{\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 QUARK models
are built from small fragments (1-20 residues long) by replica-exchange QUARK was
ranked as the No 1 server in Free-modeling (FM) in\uc1 \u160 ?}{\field \fldedit
{\*\fldinst {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \af0 \lang1033 \langnp1033
\cf0 }{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
HYPERLINK "http://predictioncenter.org/casp9/CD/data/html/groups.server.fm.html" }}
{\fldrslt {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \af0 \lang1033
\langnp1033 \cf0 }{\fs24 \kerning2 \dbch \af5 \hich \af5 \loch \f5 \lang1033
\langnp1033 \cf1 \ul1 \highlight16 CASP9}}}{\fs24 \kerning2 \dbch \af5 \hich
\af5 \loch \af5 \lang1033 \langnp1033 \cf1 \ul1 \highlight16 }{\fs21 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \uc1 \u160 ?and\uc1
\u160 ?}{\field \fldedit {\*\fldinst {\fs21 \kerning2 \loch \af0 \hich \af0
\dbch \af0 \lang1033 \langnp1033 \cf0 }{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch
\f0 \lang1033 \langnp1033 \cf0 HYPERLINK
"http://predictioncenter.org/casp10/groups_analysis.cgi?
type=server&tbm=on&tbm_hard=on&tbmfm=on&fm=on&submit=Filter" }}{\fldrslt {\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \af0 \lang1033 \langnp1033 \cf0 }{\fs24
\kerning2 \dbch \af5 \hich \af5 \loch \f5 \lang1033 \langnp1033 \cf1 \ul1
\highlight16 CASP10}}}{\fs24 \kerning2 \dbch \af5 \hich \af5 \loch \af5
\lang1033 \langnp1033 \cf1 \ul1 \highlight16 }{\fs21 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \uc1 \u160 ?experiments. Since no global
template information is used in QUARK simulation, the server is suitable for
proteins that do not have homologous templates in the PDB library.}{\fs21 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain
\qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0
\rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain
\qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0
\rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\b1 \fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Fold
recognition or Threading }{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\lang1033 \langnp1033 \cf0 is a technique for predicting protein structures}
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 It is
useful in cases where homology modelling fails to predict quality structures}{\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard
\plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright
\lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Fold
recognition: Finding the best fit of a sequence to a set of candidate folds}{\fs21
\kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\b1 \fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
Process of threading}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 :}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar
\aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2
\hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033
\langnp1033 \cf0 In the process of }{\fs21 \kerning2 \dbch \af0 \hich \af0 \loch
\f0 \lang1033 \langnp1033 \cf0 \uc1 \u8220 ?}{\fs21 \kerning2 \loch \af0 \hich \af0
\dbch \f0 \lang1033 \langnp1033 \cf0 Threading}{\fs21 \kerning2 \dbch \af0 \hich
\af0 \loch \f0 \lang1033 \langnp1033 \cf0 \uc1 \u8221 ?}{\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 , we mount an amino acid sequence
on to the backbone of template structures in a folds library}{\fs21 \kerning2 \loch
\af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \line }{\fs21 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain
\qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0
\rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2
\loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Each step is }{\fs21
\kerning2 \dbch \af0 \hich \af0 \loch \f0 \lang1033 \langnp1033 \cf0 \uc1 \u8220 ?}
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 drag}
{\fs21 \kerning2 \dbch \af0 \hich \af0 \loch \f0 \lang1033 \langnp1033 \cf0 \uc1
\u8221 ?}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033
\cf0 along the sequence (MQVKLFTY...) through each location of each template fold}
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \line }
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 Then,
for each fold, we must compute the fitness of sequence matching that fold!}
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
Threading involves }{\fs21 \kerning2 \dbch \af0 \hich \af0 \loch \f0 \lang1033
\langnp1033 \cf0 \uc1 \u8220 ?}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0
\lang1033 \langnp1033 \cf0 passing}{\fs21 \kerning2 \dbch \af0 \hich \af0 \loch \f0
\lang1033 \langnp1033 \cf0 \uc1 \u8221 ?}{\fs21 \kerning2 \loch \af0 \hich \af0
\dbch \f0 \lang1033 \langnp1033 \cf0 the amino acid sequence through each fold in
the database}{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033
\cf0 \par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0
\par }\pard \plain \qj \li0 \ri0 \lisb0 \lisa0 \widctlpar \aspalpha \aspnum
\adjustright \lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0
{\fs21 \kerning2 \loch \af0 \hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 The
best match is computed using a scoring function}{\fs21 \kerning2 \loch \af0
\hich \af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0
\lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21
\kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0
\lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21
\kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \qj \li0 \ri0
\lisb0 \lisa0 \widctlpar \aspalpha \aspnum \adjustright \lin0 \rin0 \itap0 \fs21
\kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs21 \kerning2 \loch \af0 \hich
\af0 \dbch \f0 \lang1033 \langnp1033 \cf0 \par }\pard \plain \ql \li0 \ri0
\lisb0 \sa200 \lisa0 \sl276 \slmult1 \widctlpar \aspalpha \aspnum \adjustright
\lin0 \rin0 \itap0 \fs21 \kerning2 \dbch \af2 \hich \af0 \loch \af0 {\fs22
\kerning0 \dbch \af6 \hich \af6 \loch \f6 \lang9 \langnp9 \cf0 \par }}