AIVE

AIVE Result Viewer

AIVE Result

Target virus
PDB file
PAE JSON file
① 3D Structure Prediction
1. The PAE is a value that estimates the difference between the relative locations of two residues of the model and the real model. The value has a negative correlation with the accuracy of the pairwise position of two residues. As the PAE value decreases, the accuracy increases and vice versa.
2. The pLDDT is a value that estimates the reliability of the model. The value indicates the likelihood of folding of the protein structure at that location, with higher values indicating a greater likelihood of folding.
DockQ :
② Structure difference graph according to position
1. Protein structure prediction characteristics (SCPS: SubClustering of Protein Structure in ①) and polarity (PS: Polarity Score) are shown.
2. SCPS divides the residues constituting the 3D protein structure into several groups using K-means clustering. The indicated groups are those with a high proportion of WHO name variants.
3. PS assigns weight to a position having a specific structure (where P appears consecutively) by polarity features of amino acid.
③ Graph of rate of change according to position
1. Ratio change in frequencies of amino acids sequences (mr: mutation rate) and Biochemical properties of amino acid sequencies (bpes: biochemical properties eigen score) are shown
2. MR is the rate of change of Amino Acid and its constituent nucleotides; the higher the rate, the higher the rate of change.
3. BPES measures changes in the biochemical properties of amino acids at the site of a mutation. A high rate of change results in a high BPES value. Biochemical properties are measured by integrating amino acid residue, PH, and hydrophobic information.
④ APESS score according to position
1. APESS is an amino acid property eigen selection score calculated by multiplying the values of SCPS, PS, MR, and BPES.
2. APESS is a value that integrates the results of ② and ③. The higher the APESS value, the more dangerous the mutation is.
3. The graph shows the positions of mutations with structural differences (SCPS, PS) in viral proteins. It also shows the positions and magnitudes of relatively large physical changes (MR) and biochemical changes (BPES).
⑤ APESS score distribution graph
1. The following graph shows the APESS score distribution of mutations generated through random sampling. The red area belongs to the quantile set of 0.05, signifying that the mutation is risky if it belongs to this area. A lettered balloon indicates the score position of the WHO VOC variant, and the red flag indicates the APESS score position of the protein predicted in ①.

⑥ Virus amino acid info

Visualizes and tabulates changes in repeated polarity structure sequence for wild-type sequences and mutated type sequences used in ①.

Sequence without mutations (Reference)

Sequence with mutations (Mutation)

Polarity feature			Amino acid
Polarity features	Non-Polar	N	Ala (A), Val (V), Leu (L), Gly (G), Ile (I), Met (M), Trp (W), Phe (F), Pro (P)
	Polar	P	Ser (S), Cys (C), Asn (N) , Gln (Q), Thr (T), Tyr (Y)
	Acidic	A	Asp (D), Glu (E)
	Basic	B	Lys (K), Arg (R), His (H)
Five amino acid properties	Amino acids with electrically charged side chain_negative	1	Lys (K), Arg (R), His (H)
	Amino acids with electriccally charged side chain_positive	2	Asp (D), Glu (E)
	Amino acids with Polar uncharged side chain	3	Ser (S), Asn (N) , Gln (Q), Thr (T)
	Special cases	4	Cys (C), Gly (G), Pro (P)
	Amino acids with hydrophobic side chain	5	Ala (A), Val (V), Leu (L), Ile (I), Met (M), Trp (W), Phe (F)

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Mutated Virus AA Seq

Amino acids with electriccally charged side chain _Negative	R H K
Amino acids with electriccally charged side chain _positive	D E
Amino acids with Polar uncharged side chain	S T N Q
Special cases	C G P
Amino acids with hydrophobic side chain	A V I L M F Y W