Using Computational Tools in Virtual Protein-Centric CUREs and UREs
Based on “Teasching Virtual Protein-Centric CUREs and UREs Using Computational Tools”
Introduction and Overview to the Tutorials Below
Phase 1: Developing a Research Proposal
Module 1: Using Primary Literature and Data Bases
Part 1 (Literature Background, PubMed), Part 2 (Using Blast), Part3 (Using Clustal Omega)
Module 2: Molecular Visualization
Module 3: What is a good research project: Hypothesis Development & Proposal
Phase 2: Preparing the Proteins
Module 4: Creating & Validating Models
Part 1 (Creating Mutants with PyMol), Part 2 (Creating Mutants with Phyre2), Part 3 (Refining the Structures), Part 3A(Using Galaxy Web to refine monomer and oligomer structures) Part 4 (Constructing Oligomers), Part 5 (MolProbity), Part 6 (Using Missense 3D)
Phase 3: Computational Experimental Approaches to Explore the Questions developed from the Hypothesis
Module 5: Exploring Titratable Groups in a Protein
Module 6: Exploring Small Molecule Ligand Binding
Part 1 (Submitting to SwissDock), Part 2(Exploring Clusters-PyMol & Poses-Chimera)
Module 7: Exploring Protein-Protein Interactions
Module 8: Detecting and Exploring Potential Binding Sites in a Protein
Module 9: Structure-Activity Relationships of Ligand Binding & Drug Design
Papers for Journal Clubs on the Computational Techniques Presented here:
Kelley,L.A., Mezulis,S., Yates,, C.M., Wass M. & Sternberg, M.J.E. “The Phyre2 web portal for protein modeling, prediction and analysis” Nature Protocols volume 10, pages845–858(2015) https://pubmed.ncbi.nlm.nih.gov/25950237/
Bhattacharya D “refineD: improved protein structure refinement using machine learning based restrained relaxation”.Bioinformatics. 2019 Sep 15;35(18):3320-3328. https://pubmed.ncbi.nlm.nih.gov/30759180/
Williams et al. (2018) MolProbity: More and better reference data for improved all-atom structure validation. Protein Science 27: 293-315. https://pubmed.ncbi.nlm.nih.gov/29067766/
Ramu Anandakrishnan, Boris Aguilar and Alexey V. Onufriev, "H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulation", Nucleic Acids Res., 40(W1):W537-541. (2012) https://pubmed.ncbi.nlm.nih.gov/22570416/
Aurélien Grosdidier,1 Vincent Zoete,1,* and Olivier Michielin “SwissDock, a protein-small molecule docking web service based on EADock DSS” Nucleic Acids Res. 2011 Jul 1; 39(Web Server issue): W270–W277 https://pubmed.ncbi.nlm.nih.gov/21624888/
Gaoqi Weng, Ercheng Wang, Zhe Wang, Hui Liu, Feng Zhu, Dan Li, Tingjun Hou “HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA” Nucleic Acids Research, Volume 47, Issue W1, (2019) https://pubmed.ncbi.nlm.nih.gov/31106357/
Yu J, Zhou Y, Tanaka I, Yao M “Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere”. Bioinformatics. 2010 Jan 1;26(1):46-52. https://pubmed.ncbi.nlm.nih.gov/19846440/
Using Computational Tools in Virtual Molecular Biology Laboratories
Bioinformatics Workshop Template
Rubrics
Rubric for Noncovalent interactions
Rubric for Hypothesis Development and Proposal
Hints for Using Virtual Communication Approaches to Build a Research Community