NIAS

NIAS is a server to analyze the conformational preferences of amino acid residues in proteins. It is built using the Angle Probability List (APL), which represents the normalized frequency of observed pairs of amino acid residues and secondary structure in the Protein Data Bank. It combines the conformational preferences of amino acid residues (aa, torsion angles) in proteins with their secondary structure information (ss). A higher frequency associated with a pair of phi and psi angles indicates that this combination is more common in nature. The following Ramachandran maps show the conformational profile of Glycine residue when in coil, extended conformation and alpha helix secondary structure (APL1) according to the five structure databases considered by NIAS.

1. Inform an email address and the Job ID to receive the APL results. Please, enter you Institution (if applicable).

2. Inform the target amino acid sequence. The target sequence must be in one CAPITAL, and using the ONE letter code format, for example, "FNAAANF. The table below lists the letters corresponding to each amino acid.

   Amino Acid	1-Letter
   Alanine	A
   Arginine	R
   Asparagine	N
   Aspartic acid	D
   Cysteine	C
   Glutamine	Q
   Glycine	G
   Histidine	H
   Isoleucine	I
   Leucine	L
   Lysine	K
   Methionine	M
   Phenylalanine	F
   Proline	P
   Serine	S
   Threonine	T
   Tyrosine	Y
   Valine	V

3. Inform the secondary structure content of the target amino acid sequence. The secondary structure content must be in one-letter code according to the standard adopted by STRIDE, as listed represented in the table below. Note: NIAS can not recognize heterogeneous secondary structure sequences. Thus, if your sequence is composed by, for example, HHHHE, you need to simplify it to HHHHH.

   Secondary Structure	1-Letter-Code
   Alpha helix	H
   3-10 helix	G
   PI-helix	I
   Extended conformation	E
   Isolated bridge	B or b
   Turn	T
   Coil (none of above)	C

4. Select the APL Structure:

   • APL1: The target set of aa1, ..., n and ss1, ..., n is used to search in the APL Database and built the APL with the relative frequency of occurrence for each pair aa, ss.

   • APL2: The APL2 is the Single Neighbor-Dependent Angle Probability List. In the APL2 instead of using only one pair (aai,ssi) the Neighbor-Dependent pair is used (aai,ssi) (aai+1, ssi+1). With this approach we have two files, the first one returns the relative frequency of occurrence of the pair at left (aai,ssi) with the influence of the pair at right (aai+1, ssi+1). The other one returns the relative frequency of occurrence of the pair at right (aai+1, ssi+1) with the influence of the pair at left (aai, ssi).

   • APL3: The APL3 is the Complete Neighbor-Dependent Angle Probability List. In the APL3 both pairs from left (aai-1, ssi-1) and right (aai+1, ssi+1) have influence in the middle pair (aai,ssi). This approach has less occurrences than APL2, which has less occurrences than APL1.

   • APL5: This APL uses only the amino acid central with any combination of amino acids in the neighbors, but maintaining the full secondary structure target.

   • APL7: This APL uses only the amino acid central with any combination of amino acids in the neighbors, but maintaining the full secondary structure target.

   • APL9: This APL uses only the amino acid central with any combination of amino acids in the neighbors, but maintaining the full secondary structure target.

5. Select a database. Five database are available for generating the conformational profiles:

   • CullPDB Benchmark [Resol <= 3.0] - 16.475 structures
     Download the PDB list

   • Solid NMR [FS >= 400 MHz] - 146 structures
     Dowload the PDB list

   • X-Ray [Resol <= 2.5; R-Factor = 20] - 23.524 structures
     Download the PDB list

   • X-Ray [Resol <= 4.0; R-Factor = 20] - 24.199 structures
     Download the PDB list

   • Electron Crystallography - 212 structures
     Download the PDB list

   • Solution NMR [FS >= 400 MHz] - 12.793 structures
     Download the PDB list

   • Solution NMR [FS >= 600 MHz] - 11.568 structures
     Download the PDB list

   • Solution NMR [FS >= 800 MHz] - 5.810 structures
     Download the PDB list

   • EM [Resol <= 4] (AG) - 7.632 structures
     Download the PDB list

   • EM [Resol <= 10] (AG) - 10.466 structures
     Download the PDB list

   • X-Ray [Resol <= 2.5; R-Factor = 20; NR] - 12.588 structures
     Download the PDB list

   • X-Ray [Resol <= 4.0; R-Factor = 20; NR] - 13.020 structures
     Download the PDB list

6. Submit :D

   When the process it is over, you will receive an email with a Download link to your files.

   Each APL selected will be separated in one folder, with the exception of APL2 which will generated one folder for left neighbor and one folder for right neighbor as explained in 'NIAS Structure'.

   For each strip of the target sequence, based on the length of APL, will generate an APL file and one Ramachandran Plot. The structure of APL file is presented below.

   Example

   File A_H_histogram.dat represents the APL for the Alanine (A) amino acid with alpha-Helix (H) secondary structure.

   File KA_TT_histogram.dat from folder "Right" represents the APL for the Alanine (A) amino acid with Turn (T) secondary structure with influence of a Lysine (K) in also in Turn (T) secondary structure.

   File KA_TT_histogram.dat from folder "Left" represents the APL for the Lysine (K) amino acid with Turn (T) secondary structure with influence of a Alanine (A) in also in Turn (T) secondary structure.

   File QAK_EEE_histogram.dat represents the APL for the Alanine (A) amino acid with beta-Sheet (E) secondary structure round by a Lysine (K) in beta-Sheet (E) secondary structure and a Glutamine (Q) also in Beta-Sheet (E) secondary structure.

   File A_EEEEC_histogram.dat represents the APL for the Alanine (A) amino acid with beta-Sheet (E) secondary structure round by two beta-Sheet (E) secondary structure from left and a beta-Sheet (E) secondary structure and coil (C) secondary structure from right.

   In each \*\_histogram.dat file, we have 4 major groups where the last group is subdivided in sets of [OMEGA, CHI's, Protein_ID]:

   PHI PSI Frequency [[OMEGA, CHI's, Protein_ID],]

   Example

   QAK_EEE_histogram.dat
   PHI PSI Freq. [[OMEGA, CHI's, Protein_ID],]
   -103.000000 168.000000 0.100000 [[175.5, 999.9, 999.9, 999.9, 999.9, '3RHTC'] ,]
   
   \*\*\*The value 999.9 represents the amino acid with no CHI angle.
   

If you have any questions, please contact Prof. Dr. Marcio Dorn: mdorn@inf.ufrgs.br

If you use NIAS in a scientific publication, we would appreciate citations to the following paper:

BibTeX

@article{Borguesan2017,
    author = {Borguesan, Bruno and Inostroza-Ponta, Mario and Dorn, Márcio},
    title = {NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins},
    journal = {Journal of Computational Biology},
    volume = {24},
    number = {3},
    pages = {255-265},
    year = {2017},
    doi = {10.1089/cmb.2016.0074},
    note = {PMID: 27494258},
    URL = {https://doi.org/10.1089/cmb.2016.0074},
    eprint = {https://doi.org/10.1089/cmb.2016.0074}
}