Jurica Novak, Center for Informatics and Computing, Ruđer Bošković Institute

This readme.txt file was generated on 20250305 by Jurica Novak

GENERAL INFORMATION

1. Dataset Title: In Silico Design of Alkhumra Virus NS3 Protease Inhibitors

2. Research Project Title: Drug Repurposing for Viral Hemorrhagic Fevers

3. Author Information:
     A.   Principal Investigator Contact Information:
            Name: Jurica Novak
            Institution: Center for Informatics and Computing, Ruđer Bošković Institute
            Address: Bijenička cesta 54, Zagreb, Croatia
            Email: jnovak@irb.hr

4. Dates (Suggested Format: YYYYMMDD):
     A.   Data Collection Date: 2025
     B.   Research Start and End Dates: 2025
     C.   Time Period Covered by the Data: 2025

5. Geographical Location of Data Collection: Croatia

6. Funding Sources Supporting Data Collection: UniRi project Uniri-mladi-prirod-22-8

CONTENT INFORMATION

1. Data Description:  Molecular dynamics (MD) simulations of the Alkhumra virus protease and protease-drug complexes.

2. Keywords:   Alkhumra; protease; NS3; NS2B/NS3; drug repurposing; molecular docking; molecular dynamics

3. Research Data Dictionary (records and explains variables, units of measurement, value ranges, allowed values, missing values, methods, scales, file formats, notes):

ACCESS AND SHARING INFORMATION

1. Licenses/Restrictions on Research Data: Open access

2. Link to Publications Citing or Using the Research Data: Manuscript preparation is in progress for the article "In Silico Design of Alkhumra Virus NS3 Protease Inhibitors."

3. Links to Publicly Available Research Data:

4. Links to Supplementary Datasets:

5.  Are Data Derived from Another Source? No

6.  Citation of Research Data (provide citation format example):

7.  Research Data Formats:
        mdcrd - Amber trajectory output file
        prmtop - Amber parameter file
        rst - Amber restart file
        out - Amber output file
        info - Amber info file

OVERVIEW OF RESEARCH PROJECT DATA AND FILES

1.  Folder List:
        NS3 - MD trajectory of NS3 (His37+/Asp61-/Ser121-)
        NSNS2B/NS3 - MD trajectory of NSNS2B/NS3 (His37+/Asp61-/Ser121-)
        NS3_HIS0_SER0 - MD trajectory of NS3 (His37/Asp61-/Ser121)
        DB00696 - MD trajectory of NSNS2B/NS3:DB00696 complex
        DB01879 - MD trajectory of NSNS2B/NS3:DB01879 complex
        DB04016 - MD trajectory of NSNS2B/NS3:DB04016 complex
        DB06817 - MD trajectory of NSNS2B/NS3:DB06817 complex
        DB11611 - MD trajectory of NSNS2B/NS3:DB11611 complex
        DB11852 - MD trajectory of NSNS2B/NS3:DB11852 complex
        TRAJ_1, TRAJ_2, TRAJ_3 - triplicates 1, 2, 3

2.  File List (list all dataset files with a brief description):
        min* - system minimization
        heat* - heating trajectory
        ekvi* - equilibration trajectory
        md* - production trajectory
        noions* - stripped trajectory (without water and ions)

3.  Relationships Between Files:

4.  Additional Related Data:

5.  File Naming Convention (e.g., <project acronym><method><location><version or date>.<extension>):

6.  Are There Multiple Versions of the Dataset? No
     A.   If yes, file name of the updated version:
            Why was the file updated?
            When was the file updated?
            Who updated the file?

DATA COLLECTION AND PROCESSING INFORMATION

1. Description of Methods Used for Data Collection/Generation:  Results obtained using the Amber 22 molecular dynamics package.

2. Data Processing Methods:

3. Software or Instrument-Specific Information for Data Interpretation: Amber 22

4. Data Anonymization Procedures:

5. Quality Assurance Procedures Applied to Data:

6. Individuals Involved in Data Collection, Processing, and Analysis: Jurica Novak

SPECIFIC DATA INFORMATION FOR <FILE AND/OR DIRECTORY NAME>

(Repeat this section for each dataset, file, or directory as necessary.)

1. Number of Variables:

2. Number of Cases/Rows:

3. List of Variables (list variable names, descriptions, units, and value labels):

4. Missing Data Information:

5. Specialized Formats Used: