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AlphaFold 3 serverZOOM links:
PMI Muscle Club (CRB 702, TUE at 12 pm)
Cell Motility Journal Club zoom (CRB 702, WED at 12 pm)
Lab Meeting zoom (CRB 702, Mon at 4 pm)
UPENN zoom
Databases and General Protein Resources
- ExPASy General Protein Resources
- NCBI Protein Databases and Resources
- EBI European Bioinformatics Institute, General Protein Resources
- Pole Bio-Informatique Lyonnais General Protein Resources
- BIOPLEX database
- UniProt Universal Protein Resource
- PDB Protein Data Bank
- PDBe Protein Data Bank Europe
- dbPTM protein post-translational modifications
- EMDB The Electron Microscopy Data Bank
- The Human Protein Atlas Tissue Specific Expression Profiles of Human Proteins
- UCSC Human Gene Sorter Exploring gene families and expression level
- BioGPS Gene expression level databases for various tissue
- A Protein Modification Resource
- Phospho.ELM Database of S/T/Y phosphorylation sites
- PhosphoSitePlus protein modification resource
- Science Tools
- IDT gBlocks
- ProtΠ
- EMPIAR cryo-EM data deposition service
- Procleave prot cleavage site pred basssed on PDB
- PeptideCutter
- ProtParam
- Translate
- Reverse Translate
- Prosper
Molecular Biology and Kinetics Tools
- ATCC Biological material resource
- Addgene Plasmid repository
- Dharmacon Collection of cDNAs and ORFs
- DNAsu Plasmid repository
- Tenua Kinetics Simulation Program
Crystallography and Molecular Visualization Software and Databases
- MATTPROB Matthews Coefficient (Vm) Probability Calculation
- HKL Research X-ray Data Processing
- XDS/XSCALE X-ray Data Processing
- SnB Direct-Methods Software Determination of Crystal Structures
- SHELX Suite of Programs for Crystal Structure Determination
- PHENIX Automated determination of macromolecular structures using X-ray crystallography
- CCP4 Crystallography Software Suite
- Coot Model Building, Validation and Refinement
- PyMOL Molecular Visualization
- SHARP/BUSTER Structure Phasing Software
- MF converter molecular formats converter
- Cryo-EM Software Tools For Molecular Microscopy
- Chimera Molecular Visualization
- Crystallographic Software list
- Cryo-EM software list
- Spider Solvent Protein-Protein Interface iDEntification and Recognition
Lab tools
- Benchling oligo design
- Centrifuge Rotor Speed Calculator
- Molarity Calculator
- Concentration Calc
- Biorender
Crystallographic Databases
- Anomalous Scattering X-ray Anomalous Scattering Resources
- Heavy-Atom Databank Heavy Atom Derivatives Resources forthe Solution of Protein Structures
- Heavy Atom Reactivity Table Heavy Atom Reactivities with amino acids
Protein Sequence and Structure Analysis
Alignment
- BLAST
- Sequence Manipulation Suite
- FASTA converter
- Clustal W Multiple Sequence Alignment
- Clustal Ω Multiple Sequence Alignment
- ESPript Multiple Sequence Alignment
- Jalview Multiple Sequence Alignment Editor
- T-Coffee Multiple Sequence Alignment
- ScoreConsA program to score residue conservation in a multiple sequence alignment
- SIAS Sequence Identity And Similarity
- WebLogo Sequence Aligment representation
2D-Structure Analysis
- DeepCoil Prediction of Coiled Coil
- Jpred Sequence Analysis and Structure Prediction
- HCA Hydrophobic Cluster Analysis
- PairCoil2 Prediction of Coiled Coil
- PDB2PQR Protein electrostatics
3D-Structure Analysis
- PPI3D searching, analyzing, modeling protein interactions
- 3DView pdb viewer
- iCn3D pdb viewer
- FirstGlance in Jmol pdb structure analysis
- DynDom Protein Domain Movement Analysis
- PolyPhen-2 prediction of functional effects of human nsSNPs
- CATH Protein Structure Classification
- Consurf Analysis of Surface Conservation in Protein Structures
- Dali Protein Structure Analysis and Structural Homology Identication
- HHpred Homology Detection and Structure Predictions
- I-TASSER Protein Structure and Function Prediction
- Modeller Homology or comparative modeling of protein three-dimensional structures
- PISA Interactive tool for the exploration of macromolecular interfaces
- Phyre2 Protein Homology Recognition Engine
- Phyre2 (expert mode)
- PROMALS3D Structure-Based Sequence Alignment
- RaptorX Protein Structure and Function Prediction
- SSM Secondary Structure Matching and Protein Structure Comparison
- LS-align Ligand structural aligment
- AlphaFold Colab
Synchrotrons and Beamlines
- APS Argonne National Laboratory(Chicago, IL)
- BioCARS Bio-Consortium for the Advanced Radiation Source
- IMCA-CAT Industrial Macromolecular Crystallography Associacion Collaborative Access Team
- BioCAT Biophysics Collaborative Access Team
- Berkley Lab Advanced Light Source (Berkeley,CA)
- CHESS Cornell High Energy Synchrotron Source (Ithaca, NY)
- NSLS II National Synchrotron Light Source (Brookhaven, NY)
Cryo-EM facilities
- Globus data management
- NCCAT New York Structural Biology Center Cryo-EM
- NCEF National Cryo-EM Facility (NCI)
- PNCC Pacific Northwest CryoEM Center
- SLAC Stanford SLAC CryoEM Center
- CryoEM Service Centers
- EMRL - UPENN
- Beckman Center - UPENN
- Beckman Center - UPENN iLab
- EMRL T12 schedule
- EMRL Vitrobot schedule
UPenn links
- PSOM events calendar
- PSOM service phone list
- Physiology Department
- BlueSkyPhysiology departmental events
- Pennsylvania Muscle Institute
- Institute of Structural Biology
- Cell Motility Journal Club
- iLab/CrossLab
- Cell Center
- BEN Business Enterprise Network
- Webmail
- PMACS Academic Computing Services
- Campus Map@Upenn
- Workday@Penn
- AirPennNet access
- VoiceMail UPENN
- DART UPENN
- CAMS
- EHRS
- Penn’s Electronic Research Notebook
- PennTEM Travel & expense management (Concur)
- PENNMed remote aaccess portal
- PENN Mail
- PENN BioRaft
- PENN Libraries poster printing
- PENN Software licencing
- PENN Business Services
- PENN Access Savings on Technology
- PENN Secure Share
- SPO Space Planning & Operations PSOM
- UPenn Core Facilities Finder
- My.Med.
- Employee Resources
- Upenn portal
- UPenn Box UPENN dropbox
- Airpennnet
- PSOM - Scheduling & Event Services
- Office365 Upenn
Other resources
- Ithenticate
- WeTransfer
- SlideMakers poster printing
- Holman Biotech Commons poster printing
X-ray/CryoEM Hardware and Tools
- ARI Art Robbins Instruments crystallisation robotics
- Bruker X-ray Detectors and X-ray Sources
- Douglas Instruments Oryx crystallisation robotics
- Hampton Research Protein Crystallization Products
- Jena Bioscience Protein Crystallization Products
- MiTeGen Crystallization, CryoEM Products
- EMS CryoEM grids
- Quantifoil CryoEM grids
- P212121Protein Crystallization Products
- Rigaku Resources
- HW crystallization center
Scientific Societies
- ASCB America Society for Cell Biology
- Biophysical Society
- ACA American Crystallographic Association
Granting Agencies