COMPUTATIONAL MOLECULAR BIOLOGY ONLINE BITS 4 UNIT VIII

PROTEIN HOMOLOGY Modeling

1. Comparative modeling is commonly referred to as __________ modeling (S)

b. homology

c. heterology

d. differential

e. optimal ans- a

2. Homology modeling is useful when a _______ structure of sequence that shares substantial similarity to the protein sequence of interest is available (S)

c. 2D

d. 3D

e. 1D

f. opposite ans- b

3. In comparative modeling (S)

d. the efficiency of the alignment substantially effects the accuracy of the subsequent structure prediction

e. the efficiency of the alignment substantially does not effects the accuracy of the subsequent structure prediction

f. the efficiency of the alignment shows opposite effect on structure prediction

g. structure prediction is by multiple alignment only ans- a

4. 'Fluorescence anisotropy' protein structure determination method is used to obtain(S)

e. high resolution

f. translational diffusion

g. rotational diffusion

h. spectroscopic resolution ans- c

5. Homology modeling combines ________ &________ to predict 3D structures (S)

f. Sequence analysis & N M R

g. Molecular and X-ray studies

h. Sequence analysis and molecular modeling

i. NM R and microscopy ans- c

6. Cn3D and Rasmol are the best software's for (M)

g. Molecular visualization

h. homology

i. lipids

j. carbohydrates ans- a

7. Cn3D requires ASN1 structural data as formatted by ________ rather than PDB format data as sent by SWISS-model (M)

h. NCBI

i. PDB

j. SWISS PROT

k. PEARL ans- a

8. Homology models are unlike to be useful in drug design unless the sequence identity with the template is (M)

d…> 70% ans- d

9. One of the following is not important for homology modeling

j. Oligo nucleotides (H)

ans-a

10. _______ homology model is made in 1998 from sequences in Swiss-prot/ TrEmbl using the SWISS - MODEL routines (H)

c.3D CRUNCH

ans- c

PROTEIN THREADING

1.Threading ia a method for __________recognition (S)

c.fold

ans- c

2. In Threading ________ is matched with______(S)

a. sequence , protein shape

ans- a

3. _______ method is used in absence of any substantial sequence identity to proteins to known structures (S)

c. threading

ans- c

4. _______ method cannot work in absence of protein, structures that have substantial sequence similarity to the protein sequence of interest (S)

a. comparative modeling

ans- a

5. Scoring in Threading is carried out by (S)

c. mapping the structural information to create a profile for each structural site

ans- c

6. _________ are the essential components of Threading (M)

d. optimal alignment & scoring ans- d

7. Threading approaches may be on (M)

b. sequence & structural information

ans- b

8. Threading technique is also used in _________ (M)

c. CASP 2 & 3

ans- c

9. Protein Threading is a ________ type of method (H)

c. 3D - 1D fold recognition

10. 3D-PSSM, HHpred, Robetta are the common software tools for ________ method

b. protein Threading

ans- b

PROTEIN Ab initio STRUCTURE PREDICTION

1. Ab initio method attempt to predict protein structure from first principles using theories from________ (S)

a. statistical thermodynamics and quantum mechanics

ans-a

2. Ab initio folding is often interpreted based on (S)

b. Physiochemical interactions

ans-b

3. PDB and MSD are______________ (S)

c. Primary protein structure database

ans-c

4. Ab initio is otherwise called as _________ protein modeling(S)

a. de novo

ans-a

5. Ab initio protein modeling methods seek to build 3D protein models based on (S)

b. physical principles

ans-b

6. With the help of computational resources like blue gene or MDGRAPE-3 _______ protein structures are predicted (H)

c. large

ans-c

7. As an intermediate step towards predicted protein structures ________ predictions have been proposed (M)

d. contact map ans-d

8. Threading is a ______________ modeling(M)

b. comparative

ans-b

9. a helix and b sheet structure were suggested by __________(M)

b. Linus Pauling

ans-b

10. _________method consist in modeling all the energetics involved in the process of folding and then in finding the structure with lowest free energy (H)

a. Ab initio

ans-a

PROTEIN DESIGN EMPHASIS ON STRUCTURAL BIOINFORMATICS

1. The search space is pruned by the assumption that the protein in question adopts a structure that is reasonably close to the structure of atleast one known protein in ______

Structure prediction (H)

c. comparative

2. Most de novo structure prediction methods rely on simplified representation of the proteins (H)

a. atomic structure if

ans-a

3. Assumption of homology modeling is _________ (S)

a. two homologous proteins will share very similar structure

ans-a

4. _________ angles determine side chains orientations (S)

a. dihedral

ans-a

5. Rotamers are the side chain conformations with_________ (M)

a. high energy

ans-b

6. Side chain geometry prediction are useful for analyzing the protein___________(S)

b. hydrophyllic core

ans-a

7. MODELLER is a popular software tool for producing_________ (M)

b. NMR spectroscopy

ans-b

8. ________ method is used to predict the structure of complexes of two or more proteins

d. protein-protein docking ans-d

9. Alanine is ____________ in nature (S)

a. hydrophobic

ans-a

10. Single letter code for Glutamine is (S)

c. Q

ans-c

5.

1. _________ approach is based on thermodynamic hypothesis (S)

c. ab initio

ans-c

2. Torsion angles are(S)

a. phi, psi and omega

ans-a

3. In Rosetta method, tertiary structures are generated by minimizing a scoring function that accounts for(H)

c. non-local interaction

ans-c

4. Fully automated predictions with no human intervention are studied in a CASP parallel project known as (S)

d. CAFASP ans-d

5. The first step of homology modeling is identification of best template structure by_______ simple method (S)

c. FASTA and BLATS

ans-c

6. _________method divided the target into a series of short segments each of which is matched to its own template fitted from the PDB (M)

a. segment matching

ans-a

7. Regions of the target sequence that are not aligned to a template are modeled by________(M)

c. loop modeling

ans-c

8. The low identity region in protein modeling is referred as (M)

b. twilight zone

ans-b

9. Most common and large scale sources of error in homology modeling is __________(H)

a. poor template selection

ans-a

10. Expand GRAIL (S)

a. gene recognition and analysis internet link

ans-a