Protein Input

The protein Input is a string depicting the Amino Acids. The string must be limited to a sequence of 1000 Amino Acids. As the model was not trained on sequences longer than 1000, the program will not be able to take any inputs longer than 1000 Amino Acids.

Each character in the string represents an Amino Acid. The Amino acids recognized by the program are just ACDEFGHIKLMNPQRSTVWY, where each character represents it's FASTA code for an Amino Acid. The FASTA code for Amino Acids can be found in the table below.

Code	Amino Acid	Code	Amino Acid	Code	Amino Acid	Code	Amino Acid	Code	Amino Acid
A	Alanine	B	Aspartic Acid (D) or Asparagine (N)	C	Cysteine	D	Aspartic Acid	E	Glutamic Acid
F	Phenylalanine	G	Glycine	H	Histidine	I	Isoleucine	J	Leucine (L) or Isoleucine (I)
K	Lysine	L	Leucine	M	Methionine / Start Codon	N	Asparagine	O	Pyrrolysine (Rare)
P	Proline	Q	Glutamine	R	Arginine	S	Serine	T	Theroine
U	Selenocysteine (Rare)	V	Valine	W	Tryptophan	Y	Tyrosine	Z	Glutamic Acid (E) or Glutamine (Q)

Nucleic Acid Input

The Nucleic Acid is a string depecting either your DNA or RNA. The string must be limited to a sequence of 75 Bases. As the model was not trained on sequences longer than 75, the program will not be able to take any inputs longer than 75 bases.

Each character in the string represents a Nucleotide. The Nucleotides recognized by the program are just ATGCU, where

• A is Adenine
• T is Thymine
• G is Guanine
• C is Cytosine
• U is Uracil

Mutations

With the mutations input, you can make changes to the protein sequence, and compare its Binding Free Energy with the original protein sequence.

You can give the mutations with specific commands. For multiple mutations, you can give multiple commands, all separately commas.

There are two kinds of mutations that can be done,

1. Deletions: Removes an Amino Acid
2. Replacements

Deletions

In order to delete a protein, you tell del followed by the Amino acid and it’s position.

For example, if I have an Amino Acid sequence ATCHVWTUVPRQATCHTRRRRACDEF and wanted to delete C at the third position, the command would be delG3

Sequence deletions are also supported. In order to delete a sequence of proteins, you tell del, followed by the start position and it’s amino acid, and the last position and its amino acid separated by a hyphen.

For example, if I wanted to delete the sequence of proteins from the T in the 2nd position, to the V in the 9th position, the command would be delT2-V9

Replacement

In order to replace a protein, you tell the Amino acid, it’s position, and the new amino acid.For example, if I have an Amino Acid sequence ATCHVWTUVPRQATCHTRRRRACDEF and wanted to Replace C at the third position with a T, the command would be C3T

You can also replace a single amino acid with a sequence of amino acids. It follows the same syntax, and in place of the new amino acid, you give the sequence of amino acids.

For example, if I wanted to replace the V at the fifth position with the sequence TUV, the command would be V5TUV

Giving multiple Mutation Commands at once

In order to give multiple mutation commands, you type them in the box seperated by commas.

Suppose I wanted to Delete T at 17th position, while replacing V at 5th position with TUV, the combined command would be delT17, V5TUV