1. Dhanvantari GenOME to hit

2. Flowchart Chemgenome Bhageerath H / RM2TS+ Cavity known Yes
A..A Sequence
Protein + Cavity
Genome Seq
Bhageerath H /
RM2TS+
Database FDA, ZINC, NRDBSM, NCI or Customized Database
Cavity known
Yes
RASPD Method1
Protein 3D Str
ProtSAV/ Native RMSD/ Refine Str No
Customized Drug
Protein 3D Str
AADS
RASPD Method 2
ParDOCK
Drug Structure
ADMET Filters
Final Leads

3. Input Whole Genome Sequence
Dhanvantari
Genome
Proteome
Leads
Filters (ADMET)
Input Whole Genome Sequence
>gi test organism whole genome sequence
ATGCCTTGGCCGGCCCTCGCCACATGTCACACACACAAGTGTGTGTGCACCCCCCCCCCCGTGTCCCCCTATCCCAAACCCTT
Browse
Proceed

4. Result of Genome
Top ORFs found in all 6 reading frames using Chemgenome 3.0
List 1 (top 5 a.a seqs) List 2 (top 10 a.a seqs) Select All a.a seqs
ORF Reading Genome Amino
Frame Seq. Len Seq
ORF AQRSDL…
ORF VDKLIK... .
Go for Detail View on Results
Result POPUP for Chemgenome 3.0
Back
Proceed

5. Input Protein Sequence
Dhanvantari
Genome
Proteome
Leads
Filters (ADMET)
Results from Genome Step (user can check A.A sequence from there) or
Input Protein Sequence
>Protein sequence of test organism
SCMSGRPRMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYVARHYSRAKTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRIAASASASNST
Browse
Proceed

6. Result of Proteome Best Five Models built using BHAGEERATH H
Model 1 Model 2 Model 3 Model 4 Model Select All
Go for Structure Evaluation
Model Rank Protsav Native
Score RMSD
Model A
Model A .
Result POPUP for Structure Evaluation
Refine Models
Runs Refinery Program backend
Download Zip File Results
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Proceed

7. Result of Proteome Results RM2TS+
Model 1 Model 2 Model 3 Model 4 Model Select All
Class 1 Class Class 3 Class 4 Class 5
Go for Structure Evaluation
Refine Models
Runs Refinery Program backend
Download Zip File Results
Back
Proceed

8. Input Protein Structure (PDB Format)
Dhanvantari
Genome
Proteome
Leads
Filters (ADMET)
Results from Proteome Step (Chose Protein structure) or
Input Protein Structure (PDB Format)
ATOM N MET A
ATOM CA MET A
ATOM C MET A .
Browse
Find Active Site *
If active site is known click proceed
Proceed

9. Result of Lead (STEP1: AADS)
Best Ten cavities using AADS
Cavity 1 Cavity 2 Cavity 3 Cavity 4 Cavity 5
Cavity 6 Cavity 7 Cavity 8 Cavity 9 Cavity 10
Go for Cavity Analysis
POPUP for Cavity Analysis and neighboring residues
Download Zip File Results
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Proceed

10. Input Protein-Ligand Structure (PDB Format) Submit to Run Screening
Dhanvantari
Genome
Proteome
Leads
Filters (ADMET)
Chose Database:
ZINC DB NRDBSM NCI User Defined DB FDA
POPUP for Customized DB
Browse
Input Protein-Ligand Structure (PDB Format)
ATOM N MET A
ATOM CA MET A
ATOM C MET A
TER
HETATM…
Apply filters
Browse
Apply Filters
All 5 Lipinski’s Rule
No. of Donors
No. of Acceptors
Log P limit
Molar refractivity
FC Range
Submit to Run Screening
Back
Proceed
If want to do direct docking click proceed

11. Result of Lead *(STEP2: RASPD)
Best ZINC molecules as per RASPD
ZINC {LIST OF MOLECULES}
ZINC
ZINC
ZINC .
Download Zip File Results
POPUP ZINC link
ParDOCK
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Proceed

12. Input Protein-Ligand Structure (PDB Format)
Dhanvantari
Genome
Proteome
Leads
Filters (ADMET)
Drug Molecule:
Input Protein-Ligand Structure (PDB Format)
ATOM N MET A
ATOM CA MET A
ATOM C MET A
TER
HETATM…
Browse
HETATM … .
Browse
Back
Proceed

13. Result of Lead Step 3 (ParDOCK)
Docking Score based on Binding Energy calculated by ParDOCK
Proposed Lead molecules with Binding Poses
ZINC Energy Pose1 Pose2 Pose3 Pose 4
ZINC Energy Pose1 Pose2 Pose3 Pose 4
ZINC Energy Pose1 Pose2 Pose3 Pose 4 .
POPUP ZINC link
POPUP Pose 1 View
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Proceed

14. An additional ADMET calculator could be added

15. ADMET SCORE Calculator
Dhanvantari
Genome
Proteome
Leads
Filters (ADMET)
ADMET SCORE Calculator
Input ligand
Browse
Absorption
Distribution
Metabolism
Excretion
Toxicity
Total score:
Back
Proceed

16. Final Leads Rank Molecule Energy(kcal/mol) ADMET Score
1 ZINC Energy ADMET Score
2 ZINC Energy ADMET Score
3 ZINC Energy ADMET Score .
POPUP ZINC link

17. Thank you