final edits

docs/index.md

@@ -1,6 +1,5 @@
-# iDEC 2022 | DU_DTU_NSUT-Delhi
 
-### In-silico directed evolution of Laccase enzyme to enhance its stability and catalytic efficiency in the degradation of Aflatoxin B1 and Aflatoxin G1
+## In-silico directed evolution of Laccase enzyme to enhance its stability and catalytic efficiency in the degradation of Aflatoxin B1 and Aflatoxin G1
 
 **Mycotoxins** are secondary metabolites of fungi that cause hepatotoxicity, teratogenicity, and immunotoxicity, and are classified as group I carcinogens. Aflatoxins (AFs)  are a type of mycotoxin produced by fungal species such as Aspergillus flavus, and A. parasiticus. 
 These commonly infect cereal crops, including wheat, tree nuts, maize, cotton, and peanuts, and can pose serious threats to humans and animals by causing various complications such as hepatotoxicity, teratogenicity and immunotoxicity. *The main aflatoxins are B1, B2, G1 and G2, and can be toxic to the body through inhalation, mucous membranes or skin,leading to an overactive inflammatory response.*

docs/project/discussion.md

@@ -11,4 +11,7 @@ From the results generated, 4 best results were filtered and their stacking effe
 
 The applications of the laccase degradation activity lies towards having safer food work and also works under the **Goal 2 -> 0 Hunger** and **Goal 3 -> Good Health and Well Being** of the Sustainable Development Goals.
 
-![SDG](./sdg.png)
+![SDG](./sdg.png)
+
+>[Sustainable Development Goals](https://sdgs.un.org/goals)
+

docs/project/references.md

@@ -1,15 +1,16 @@
-1.	Dellafiora L, Galaverna G, Reverberi M, Dall'Asta C. Degradation of Aflatoxins by Means of Laccases from Trametes versicolor: An In Silico Insight. Toxins (Basel). 2017;9(1):17. Published 2017 Jan 1. doi:10.3390/toxins9010017
-2.	Ernst, H. A., Jørgensen, L. J., Bukh, C., Piontek, K., Plattner, D. A., Østergaard, L. H., Larsen, S., & Bjerrum, M. J. (2018). A comparative structural analysis of the surface properties of asco-laccases. PLoS ONE, 13(11). https://doi.org/10.1371/journal.pone.0206589
-3.	Alberts JF, Gelderblom WC, Botha A, van Zyl WH. Degradation of aflatoxin B(1) by fungal laccase enzymes. Int J Food Microbiol. 2009;135(1):47-52. doi:10.1016/j.ijfoodmicro.2009.07.022
+1.	Dellafiora L, Galaverna G, Reverberi M, Dall'Asta C. Degradation of Aflatoxins by Means of Laccases from Trametes versicolor: An In Silico Insight. Toxins (Basel). 2017;9(1):17. Published 2017 Jan 1. [https://doi:10.3390/toxins9010017](https://doi:10.3390/toxins9010017)
+2.	Ernst, H. A., Jørgensen, L. J., Bukh, C., Piontek, K., Plattner, D. A., Østergaard, L. H., Larsen, S., & Bjerrum, M. J. (2018). A comparative structural analysis of the surface properties of asco-laccases. PLoS ONE, 13(11). [https://doi.org/10.1371/journal.pone.0206589](https://doi.org/10.1371/journal.pone.0206589)
+3.	Alberts JF, Gelderblom WC, Botha A, van Zyl WH. Degradation of aflatoxin B(1) by fungal laccase enzymes. Int J Food Microbiol. 2009;135(1):47-52. [https://doi:10.1016/j.ijfoodmicro.2009.07.022](https://doi:10.1016/j.ijfoodmicro.2009.07.022)
 4.	Kielb P, Gray HB, Winkler JR. Does Tyrosine Protect S. Coelicolor Laccase from Oxidative Degradation? ChemRxiv. 2020. doi:10.26434/chemrxiv.12671612.v1 This content is a preprint and has not been peer-reviewed.
-5.	Clemmer JD, Carr J, Knaff DB, Holwerda RA. Modification of laccase tryptophan residues with 2-hydroxy-5-nitrobenzyl bromide. FEBS Lett. 1978;91(2):346-350. doi:10.1016/0014-5793(78)81207-1
-6.	Liu Y, Mao H, Hu C, et al. Molecular docking studies and in vitro degradation of four aflatoxins (AFB1 , AFB2 , AFG1 , and AFG2 ) by a recombinant laccase from Saccharomyces cerevisiae. J Food Sci. 2020;85(4):1353-1360. doi:10.1111/1750-3841.15106
-7.	Christensen NJ, Kepp KP. Accurate stabilities of laccase mutants predicted with a modified FoldX protocol. J Chem Inf Model. 2012;52(11):3028-3042. doi:10.1021/ci300398z
-8.	Stanzione, I., Pezzella, C., Giardina, P. et al. Beyond natural laccases: extension of their potential applications by protein engineering. Appl Microbiol Biotechnol 104, 915–924 (2020). https://doi.org/10.1007/s00253-019-10147-z
-9.	Liu, Y., Mao, H., Woldemariam Yohannes, K., Wan, Z., Cao, Y., Tron, T., Lin, J., Jiang, Y., Li, H., & Wang, J. (2021). Degradation of aflatoxin B1 by a recombinant laccase from Trametes sp. C30 expressed in Saccharomyces cerevisiae: A mechanism assessment study in vitro and in vivo. Food Research International, 145. https://doi.org/10.1016/j.foodres.2021.110418
-10.	 Acharyya SR, Sen P, Kandasamy T, Ghosh SS. Designing of disruptor molecules to restrain the protein-protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques [published online ahead of print, 2022 Jun 1]. Mol Divers. 2022;10.1007/s11030-022-10462-0. doi:10.1007/s11030-022-10462-0
-11.	 Kumar P, Mahato DK, Kamle M, Mohanta TK, Kang SG. Aflatoxins: A Global Concern for Food Safety, Human Health and Their Management. Front Microbiol. 2017;7:2170. Published 2017 Jan 17. doi:10.3389/fmicb.2016.02170
-12.	Reiss, R., Ihssen, J., Richter, M., Eichhorn, E., Schilling, B., & Thöny-Meyer, L. (2013). Laccase versus laccase-like multi-copper oxidase: a comparative study of similar enzymes with diverse substrate spectra. PloS one, 8(6), e65633. https://doi.org/10.1371/journal.pone.0065633	
+5.	Clemmer JD, Carr J, Knaff DB, Holwerda RA. Modification of laccase tryptophan residues with 2-hydroxy-5-nitrobenzyl bromide. FEBS Lett. 1978;91(2):346-350. [https://doi:10.1016/0014-5793(78)81207-1](https://doi:10.1016/0014-5793(78)81207-1)
+6.	Liu Y, Mao H, Hu C, et al. Molecular docking studies and in vitro degradation of four aflatoxins (AFB1 , AFB2 , AFG1 , and AFG2 ) by a recombinant laccase from Saccharomyces cerevisiae. J Food Sci. 2020;85(4):1353-1360. [https://doi:10.1111/1750-3841.15106](https://doi:10.1111/1750-3841.15106)
+7.	Christensen NJ, Kepp KP. Accurate stabilities of laccase mutants predicted with a modified FoldX protocol. J Chem Inf Model. 2012;52(11):3028-3042. [https://doi:10.1021/ci300398z](https://doi:10.1021/ci300398z)
+8.	Stanzione, I., Pezzella, C., Giardina, P. et al. Beyond natural laccases: extension of their potential applications by protein engineering. Appl Microbiol Biotechnol 104, 915–924 (2020). [https://doi.org/10.1007/s00253-019-10147-z](https://doi.org/10.1007/s00253-019-10147-z)
+9.	Liu, Y., Mao, H., Woldemariam Yohannes, K., Wan, Z., Cao, Y., Tron, T., Lin, J., Jiang, Y., Li, H., & Wang, J. (2021). Degradation of aflatoxin B1 by a recombinant laccase from Trametes sp. C30 expressed in Saccharomyces cerevisiae: A mechanism assessment study in vitro and in vivo. Food Research International, 145. [https://doi.org/10.1016/j.foodres.2021.110418](https://doi.org/10.1016/j.foodres.2021.110418)
+10.	 Acharyya SR, Sen P, Kandasamy T, Ghosh SS. Designing of disruptor molecules to restrain the protein-protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques [published online ahead of print, 2022 Jun 1]. Mol Divers. 2022;10.1007/s11030-022-10462-0. [https://doi:10.1007/s11030-022-10462-0](https://doi:10.1007/s11030-022-10462-0)
+11.	 Kumar, P., Mahato, D. K., Kamle, M., Mohanta, T. K., & Kang, S. G. (2017). Aflatoxins: A Global Concern for Food Safety, Human Health and Their Management. Frontiers in microbiology, 7, 2170. [https://doi.org/10.3389/fmicb.2016.02170](https://doi.org/10.3389/fmicb.2016.02170)
+12.	Reiss, R., Ihssen, J., Richter, M., Eichhorn, E., Schilling, B., & Thöny-Meyer, L. (2013). Laccase versus laccase-like multi-copper oxidase: a comparative study of similar enzymes with diverse substrate spectra. PloS one, 8(6), e65633. [https://doi.org/10.1371/journal.pone.0065633](https://doi.org/10.1371/journal.pone.0065633)
+13. Zhou, Z., Li, R., Ng, T. B., Huang, F., & Ye, X. (2022). Considerations regarding affinity determinants for aflatoxin B1 in binding cavity of fungal laccase based on in silico mutational and in vitro verification studies. Ecotoxicology and environmental safety, 234, 113412. Advance online publication. [https://doi.org/10.1016/j.ecoenv.2022.113412](https://doi.org/10.1016/j.ecoenv.2022.113412)	
 
 ## Tools
 
@@ -22,6 +23,6 @@ Schrödinger Release 2022-3: Desmond Molecular Dynamics System, D. E. Shaw Resea
 6.	Mega - x - Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018;35(6):1547-1549. doi:10.1093/molbev/msy096
 7.	Pdb - Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. doi: 10.1093/nar/28.1.235. PMID: 10592235; PMCID: PMC102472.
 8.	Pymol - Seeliger D, de Groot BL. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des. 2010;24(5):417-422. doi:10.1007/s10822-010-9352-6
-
+9. https://www.un.org/sustainabledevelopment/goal-of-the-month/
 
 

docs/project/results.md

@@ -6,7 +6,7 @@ Binding energies obtained from docking of wild-type laccase enzymes yielded very
 
 `Laccase (WT) with NE`
 
-![Laccase WT with NE](./Crystallised_ligand_clean.png) 
+![Fig:1.Laccase WT with NE](./Crystallised_ligand_clean.png) 
 
 `Laccase (WT) with AFB1`
 

docs/team.md

@@ -1,14 +1,14 @@
 # Our Team
-We are a team of 5 members from **Delhi** who formed this team together in hopes of participating in iDEC and trying to learn more about the world of directed evolution. 
+We a group of 5 enthusiastic budding scientists who have come together from varying institutes in **Delhi** and have formed this team together with the ambitions of participating in iDEC and walking in the path to learn more about the world of directed evolution and everybit of applicative potential it entails. 
 ***
 Our team members are:-
-
-* Eshaan Agarwal 
-* Swaranjeet Singh
+
 * Akanksha Aggarwal
-* Prachi Singh 
+* Eshaan Agarwal (Team Lead)
 * Khushi Goel
+* Prachi Singh 
+* Swaranjeet Singh
 
-We could not get much or any mentor support and have built our idea and the data generated all on our own, and we hope to learn more and get acquainted to all iDEC teams participating. 
+We are working through open sources and sans mentorship in this project. We hope to learn more and get acquainted to all iDEC teams participating. iDEC presents a very holistic approach with an edge of competitiveness. It carries an essence of learning through practice. We are very fortunate to be a part of the iDEC competition. 
 
 

mkdocs.yml

@@ -39,12 +39,14 @@ repo_url: https://github.com/idec-teams/2022_DU_DTU_NSUT-Delhi
 copyright: Copyright © 2022 iDEC. CC-BY-4.0 | The International Directed Evolution Competition (iDEC) is a Scottish Charitable Incorporate Organisation (SCIO), registered in Scotland, with charity number：SC050826
 
 nav:
-  - Team: team.md
+  - Team: team.md 
   - Project:
-      - Background: project/background.md
-      - Project Introduction: index.md
-      - Results: project/results.md
-      - Discussion and Path Ahead: project/discussion.md
+      - Ideation:
+          - Introduction: index.md
+          - Background: project/background.md
+      - Findings:
+          - Results: project/results.md
+          - Discussion and Path Ahead: project/discussion.md
       - Documentation:
           - Protocols: documentation/protocols.md
           - Supplementary information: project/Supplementary.md