This page is where we collect resources for computational aspects of projects, amenable to remote-science .
(Read: just because the FPLC is booked this week, you can still do some science!)
If you have ideas for adding to this list, please email KAL137@txstate.edu!
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Signing electronic forms: Use Adobe Sign to securely collect electronic signatures on PDFs. (KAL prefers this method!) Here’s an excellent tutorial on how to properly prepare the PDF form for signatures within your Texas State University-provided Adobe Sign account.
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E-notebooks
Because documentation is critical!
Benchling – the preferred e-notebook for LewisKA Lab; email KAL when you sign up so she can link you to the lab resources within Benchling
RSpace (“Research Space”) – the preferred e-notebook for our collaborators and colleagues in the Kerwin Research Group
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Structure Prediction
NeurosnapAI Modeling (uses AlphaFold)
Tunnel and Cavity Prediction in Proteins
CAVER: Tunnel Prediction in Proteins
MoloVol: more cavity modeling
ParSe: our predictor of phase separation of intrinsically disordered proteins (Paiz et al 2021, Ibrahim et al 2022, Wilson et al 2023)
Other LLPS phase predictors:
Structure Visualization Tools
PyMol (and PyMol Wiki)
Chimera (and Chimera Users Guide)
Dock small molecules using the above and AutoDock Vina
3D printing
Do you have a 3D printer, or does your school have a MakerSpace? 3D print your favorite biomolecule!
PDB101: How to 3D Print Biomolecules: including a ready-to-print set of .stl files!
Thingiverse: search for biomolecules in the database for 3D print .stl files
Interactome Databases
H. sapiens: https://bioplex.hms.harvard.edu/
Arabidopsis thaliana: http://interactome.dfci.harvard.edu/A_thaliana/
Expression Profiling
NCBI Gene Expression Omnibus Profiles
Zebrafish Expression Database @ zfin.org
Tabula Muris: Single-Cell Mouse Transcriptomes
Multiple Sequence Alignments
ConSurf: The Evolutionary Conservation Server
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Computer Programming/Coding
UNIX For Beginners (MacOS command-line)
Figure Preparation
Figure Design & Composition
A Figure is Worth 1000 Words: figure preparation advice from ASBMB
Webinar: Preparing Figures for Publication, from ASBMB
Develop Adobe Creative Suite Skills
TxSt students/staff – download CC through ITAC
Tutorials: