NDLI: Protein-protein docking on molecular models of Aspergillus niger RNase and human actin: novel target for anticancer therapeutics

Content Provider	Springer Nature Link
Author	Gundampati, Ravi Kumar Chikati, Rajasekhar Kumari, Moni Sharma, Anurag Pratyush, Daliparthy Devi Jagannadham, Medicherla V. Kumar, Chitta Suresh Debnath Das, Mira
Copyright Year	2011
Abstract	The 3D models of human actin protein and A.niger RNase were designed using the templates ACTBIND (PDB ID: 3D3Z) and crystalline profilin-beta-actin (PDB ID: 2BTF), respectively in Modeller9v5. These models are testified using several validation methods including PROCHECK, ERRAT, WHAT-IF, PROSA2003 and VERIFY-3D. The stereo-chemical quality of the models was judged by Ramachandran plot with PROCHECK. The total quality G-factor −0.2, shows a good quality model. The ERRAT score for the human actin and A.niger RNase models are 86.104 and 84.615, respectively, fit well within the range of a high quality model. The ERRAT score for the templates 2BTF and 3D3Z are 91.111 and 97.391, respectively. The WHAT-IF evaluation justifies a reasonable homology model structure as none of the scores for each residue in the homology model is lower than −5.0. The energy-minimized model of human actin with PROSA reveals the Z-score value −10.52 between native conformations of the crystal structures. The VERIFY 3D average score is 0.36. All evidence suggests that the geometric quality of the backbone conformation, the residue interaction, the residue contact and the energy profile of the structures were well within the limits of reliable structures. The interaction energy of docking was calculated using the HEX server. The Etotal, lowest docked energy, and calculated RMSD values were −1.608 kcal mol−1, -8.369 kcal mol−1 and 0.617 Å, respectively. The study presented in the current project may be useful to design molecules that may have anticancer activity.
Starting Page	653
Ending Page	662
Page Count	10
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	18
Issue Number	2
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-05-12
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	A.niger RNase HEX server Human actin Modeller9v5 Novel target for cancer Protein-protein docking Life Sciences Computer Application in Life Sciences Computer Applications in Chemistry Health Informatics Biomedicine general Molecular Medicine
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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