Resources
Structure and Function
- Resource Linklists
- Literature Searches
- Genome Databases
- Large-scale Genomic/Proteomic Studies
- Sequnce Alignment
- NCBI Basic Local Alignment Search Tool (BLAST)
- Molecular Evolutionary Genetics Analysis (MEGA) Software
- Clustal Multiple Sequence Alignment
- EMBOSS (bioinformatics tools)
- TCoffee and TEspresso (combines structural and sequence alignments)
- ESPript (color alignments with secondary structure)
- Simple Modular Architecture Research Tool (SMART)
- HMMER Biosequence Analysis Using Profile Hidden Markov Models
- Domain Prediction
- HHpred Homology Detection and Structure Prediction
- Protein Homology/Analogy Recognition Engine (PHYRE)
- Pfam Protein Families Database
- NCBI Conserved Domains and Protein Classification Tools
- DisProt Prediction of Intrinsically Disordered Regions
- ANCHOR Binding Site Predictor in Disordered Regions
- DisMeta Disorder Prediction Metaserver
- Secondary Structure Prediction and Modeling
- Protein Structure Initiative (PSI) Model Portal
- PSIPred
- PHYRE
- Multiple Mapping Method with Multiple Templates (M4T)
- CaspR Comparative Modeling for Molecular Replacement
- Sequence Alignment and Modeling (SAM)
- SWISS-MODEL
- Ribosome Helix Generator
- Robetta Full-chain Protein Structure Prediction Server
- PEPstr Peptide Tertiary Structure Prediction Server
- Phobius Transmembrane and Signal Peptide Predictor
- SCRATCH Secondary Structure Protein Predictor
Cloning and Expression
- Vector Maps
- Primer Design
- Protein Expression
- Auto-Induction Method (ZY) (PMID: 15915565)
- Selenomethionine Labeling in Mammalian Cell Culture (PMID: 17001101)
- Protein Purification
- Protein Analysis
- Protein Engineering
Crystallization
- Screens and Formulations
- Phasing
- Cryoprotection
Crystallographic Resources
- Data Collection and Indexing
- Twinning
- Phasing (Heavy Atom)
- SOLVE/RESOLVE
- HKL2MAP
- SnB (Shake-and-Bake): A Direct-Methods Procedure for Determining Crystal Structures
- SHARP (atomic resolution)
- ACORN (atomic resolution)
- CRANK
- RANTAN
- SHELX
- Phasing (Molecular Replacement)
- PHASER
- MOLPREP
- AMORE
- CHAINSAW
- CNSsolve
- EPMR: Molecular Replacement by Evolutionary Search
- GLRF: General Locked Rotation Function (look for non-crystallographic symmetry)
- Density Modification and Automated Structure Determination/Building
- Model Building
- COOT (COOT Wiki)
- O: Molecular Model Building Software (O-Info Mailing List)
- MIFit
- Swiss-PDB Viewer
- Xpleo (loop building program)
- VMD: Visual Molecular Dynamics
- PRODRG (ligand parameters)
- HIC-Up: Hetero-compound Information Centre -- Uppsala
- Metal Coordination Sites in Proteins
- Make-NA Server: Nucleic Acid Model Building
- Refinement
- Structural Validation
- COOT
- PROCHECK
- JCSG (Joint Center for Structural Genomics) Quality Control and Validation Central
- ProSA-web: Protein Structure Analysis
- RCSB PDB Validation Server
- MOLPROBITY
- STAN: The Structure Analysis Server
- Verify3D Structure Evaluation Server
- ERRAT Structure Submission
- NQ-Flipper Asn/Gln Checker Server
- ValLigURL Ligand Validator
- Structural Evaluation
- Overview of Surface and Volume Programs
- LIGPLOT (plotting protein-ligand interactions)
- DIMPLOT (interactions across a dimer or domain-domain interface)
- SURFACE and AREAIMOL (accessible surface area calculations)
- MONSTER (infers non-covalent interactions in macromolecular complexes)
- VOIDOO (looks for interior cavities and active sites)
- VADAR: Volume, Area, Dihedral Angle Reporter
- 3V (volume calculation tools)
- CASTp (identification and measurements of accessible and inaccessible cavities)
- STP: Predicting Protein Binding Sites
- Dali Server: Structure Similarity
- PDBePISA: Macromolecular Interfaces
- Final Graphics
- Synchrotrons
- BioSync Guide to High Energy Data Collection Facilities
- Brookhaven National Labs
Attn of Annie Héroux
National Synchrotron Light Source
Brookhaven National Laboratory
75 Brookhaven Rd.
Upton, NY 11973 USA
Phone: (631) 344-4454
- Structural Organizations
Software
Coot - Macromolecular model building software
Figures
