We are currently upgrading the security configurations for our servers. Therefore, some of our databases and servers are currently not available. We provide the database and source code download in this designated webpage and we are sorry for any inconvenience caused. We will finish the security enhancement as soon as possible. 

(1) PolyQ2:

• Database download: database file (polyq2.sql); protein structures (pdbs.zip)
• Citing PolyQ2 database: Chen Li, Jeremy Nagel, Steve Androulakis, Christopher J. Lupton, Jiangning Song and Ashley M. Buckle. PolyQ 2.0: an Improved Version of PolyQ, a Database of Human Polyglutamine Proteins. Database, 2016, DOI:10.1093/database/baw021.

(2) KinetochoreDB:

• Database download: database file (kinetochoreNew.sql); sequence alignment (Alignment.zip); protein structures (link to kinetochoreDB/pdb.zip)
• Citing KinetochoreDB: Chen Li, Steve Androulakis, Jiangning Song and Ashley M. Buckle. KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. Database, accepted, 2016.

(3) HIVed database:

• Database download: database tables (HIVed.zip)
• Citing HIVed: Chen Li, Sri H Ramarathinam, Jerico Revote, Georges Khoury, Jiangning Song, Anthony W Purcell. HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. Scientific Reports, 2017.

(4) ProBAPred:

• Source code download: source code (Probapred.zip)
• Citing ProBAPred: Bangli Lu, Chen Li, Qingfeng Chen, Jiangning Song. ProBAPred: Inferring protein–protein binding affinity by incorporating protein sequence and structural features. Journal of Bioinformatics and Computational Biology, 2018.

(5) Protein coiled-coils dataset:

• Datasets:
  1. DataOS.fasta (AdditionalFile1_DataOS.fasta): Coiled-coil regions (with non-canonical heptads) for evaluation of coiled-coil oligomeric state prediction, used to generate Figure 2. CD-HIT has been used to ensure that this dataset has sequence similarity lower than 50% with training datasets of other CCD oligomeric state predictors (LOGICOIL, SCORER2.0, RFCoil and PrOCoil (note for PrOCoil, only PDB dataset was included and used)).
  2. DataOSCanonical.fasta (AdditionalFile2_DataOSCanonical.fasta): Coiled-coil regions (canonical heptads only) for evaluation of coiled-coil oligomeric state prediction, used to generate Figure 3. For example, heptad register 'defgabcdefga' is 'canonical' according to our definition, since there are no interruptions within the register; while heptad register 'defgabcda' is non-canonical, since 'efg' is missing after 'abcd'.
  3. DataMulticoil2.csv (AdditionalFile3_DataMulticoil2.csv): 11 coiled-coil regions (canonical heptads only) which were predicted to be coiled-coils by Multicoil2, used to generate Figure 4. The columns are "id, coiled-coil sequence, heptad, oligomeric state".
  4. DatasetCCD.fasta (AdditionalFile4_DatasetCCD.fasta): PDB sequences with/without coiled-coils for evaluation of coiled-coil region prediction, used to generate Figure 5. The sequences with headers containing "oursPositive" are the sequences with coiled-coils while those with headers containing "oursNegative" are the sequences without coiled-coils.
  5. CCAnnotation.csv (AdditionalFile5_CCAnnotation.csv): Coiled-coils annotation for the positive sequences in DatasetCCD.fasta. The columns are "PDB, chain, coiled-coil, start and end of the coiled-coils".
• Citing the study: Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M Buckle. Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Briefings in Bioinformatics, 2016.

(6) MetalExplorer:

• Datasets: datasets (datasets.zip)
• Source codes: programs (sourceCode.zip)
• Citing MetalExplorer: Jiangning Song, Chen Li, Cheng Zheng, Jerico Revote, Ziding Zhang, Geoffrey I Webb. MetalExplorer, a Bioinformatics Tool for the Improved Prediction of Eight Types of Metal-binding Sites Using a Random Forest Algorithm with Two-step Feature Selection. Current Bioinformatics, 2016.

(7) ClusterEPs:

• Datasets (dataset.zip)
• Source code (ClusterEPs.zip)
• Citing ClusterEPs: Quanzhong Liu, Jiangning Song and Jinyan Li. Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. Scientific Reports, 2016

(8) Periscope:

• Datasets (dataset.docx)
• Source code (periscope_13_May.zip)
• Citing Periscope: Catherine Ching Han Chang, Chen Li, Geoffrey I Webb, BengTi Tey, Jiangning Song, Ramakrishnan Nagasundara Ramanan. Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli. Scientific Reports, 2016.  

If you are experiencing any problems, please contact Dr. Chen Li (chen.li@monash.edu)