CysDuF: Database to decipher Cysteine post-translational modifications of Domain of Unknown Function (DUFs) proteins

How to use the CysDuF database

1.) The input for the CysDuF database webserver can be an DUF ID, Pfam ID, Species or an PDB ID. The Pfam ID is from the Pfam database1 which is a secondary database and consists of the protein families and domains. PDB ID is retrieved from the PDB database2 which is a primary database consists of the protein strucutres. dufinput 2.) The results can be downloaded in form of a CSV file, JSON file or an TXT file. pfaminput 3.) Results are also printed in a separate web page in form of an tabular column where it consists of a Pfam ID , retrieved from the Pfam database1, DUF information with the DUF ID and DUF Name, Species information of the PDB ID retrieved from the SCOPe database3, and the SCOPe database information namely the SCOPe Superfamily , SCOPe family information, Pathway associated with the DUFs protein, PDB_ID, Chain_ID retrieved from the SCOPe database where as the Cysteine Residue Number is retrieved from the PDB database2, DeepCys Predictions4 are prediction results from the DeepCys Cysteine multiple Cysteine post-translational modifications strucutre based prediction and the Buried fraction and Relative hydrophobicity (rHpy) is retrieved from the MENV5.

pdbinput

References:

  • Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A Salazar, Erik L L Sonnhammer, Silvio C E Tosatto, Lisanna Paladin, Shriya Raj, Lorna J Richardson, Robert D Finn, Alex Bateman, Pfam: The protein families database in 2021, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D412–D419.

  • Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S Goodsell, Rachel K Green, Vladimir Guranović, Dmytro Guzenko, Brian P Hudson, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlić, Chris Randle, Alexander Rose, Peter Rose, Raul Sala, Monica Sekharan, Chenghua Shao, Lihua Tan, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Marina Zhuravleva, Christine Zardecki, RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D464–D474.

  • John-Marc Chandonia, Lindsey Guan, Shiangyi Lin, Changhua Yu, Naomi K Fox, Steven E Brenner, SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D553–D559.

  • Nallapareddy V, Bogam S, Devarakonda H, Paliwal S, Bandyopadhyay D. DeepCys: Structure-based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains. Proteins. 2021 Jul;89(7):745-761.

  • Bandyopadhyay D, Mehler EL. Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment. Proteins. 2008 Aug;72(2):646-59.
  • Contact : Dr.Debashree Bandyopadhyay @BITS Pilani , Hyderabad Campus