PROFEAT - Protein Feature Server (2014)

PROFEAT is developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence and of small molecules from molecular structure.

You can choose to calculate feature vector for:

(A)Protein (B)Protein-Protein Interaction Pair

(C)Small Molecule

(D) Protein-Ligand Interaction Pair

For introduction to PROFEAT, please see the Reference Manual

In this page, PROFEAT is designed to compute feature vectrs for protein-ligand interaction (PLI) pairs from protein primary sequence and ligand structures.


upload your data, or try with our sample data

Please upload the

protein sequence, ligand SDF and protein-ligand pair files here:

Upload Proteins

File format of "Upload Proteins" section can be found HERE

Upload Ligand SDF

File format of "Upload Ligand SDF" section can be found HERE

Upload PLI pairs

File format of "Upload PLI pairs" section can be found HERE

Batch query allows maximum 500 PLI pairs

New features

Composition, transition, distribution (CTD) according to:

   (1) Protein-protein Interface hotspot propensity-Bogan

   (2) Protein-protein Interface (PPI) propensity-Ma

   (3) Protein-DNA Interface propensity-Schneider

   (4) Protein-DNA Interface propensity-Ahmad

   (5) Protein-RNA Interface propensity-Kim

   (6) Protein-RNA Interface propensity-Kim

   (7) Protein-RNA Interface propensity-Phipps

   (8) Protein-ligand binding site propensity-Khazanov

   (9) Protein-ligand valid binding site propen-Khazanov

   (10) Propensity for Protein-ligand polar and arom-Imai

   (11) Moleculaw weight

   (12) CLogP

   (13) No. of hydrogen bond donor in side chain

   (14) No. of hydrogen bond acceptor in side chain

   (15) Solubility in water

   (16) Amino acid flexibility index


The earlier version of PROFEAT can be found HERE.

How to cite our database


Citation: H.B. Rao, F. Zhu, G.B. Yang, Z.R. Li, and Y.Z. Chen. Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. Jul 1, 2011; 39(Web Server issue):W385-90.

Citation: Z.R. Li, H.H. Lin, L.Y. Han, L. Jiang, X. Chen, and Y.Z. Chen. PROFEAT: A Web Server for Computing Structural and Physicochemical Features of Proteins and Peptides from Amino Acid Sequence. Nucleic Acids Res. Jul 1, 2006; 34(Web Server issue):W32-7.

List of publications that used some of the features covered by PROFEAT

Last update by

Dec 1st, 2014


visits since November 6, 2005


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If you find any error in data or bug in web service, please kindly report it to Mr. Tao.

Dr. Chen Yuzong

Deputy Director of Center for Computational Science and Engineering
Professor in Department of Pharmacy
National University of Singapore, Singapore

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