EMBL-EBI: Bioinformatics services (several listed in this page).
ExPASy (Expert Protein Analysis System): Almost anything you need.
- ProtParam: It is tool that allows computing of various physical and chemical parameters from the protein sequence.
SCRATCH: Prediction of several properties (solvent accessibility, secondary structure, disorder, 3D structure, etc.) based on sequence.
PROTCALC: PW, Absorbance, Matthews Coefficient and charge vs. pH from the sequence.
ESPript: Easy Sequencing in PostScript, to render sequence similarities and secondary structure information from aligned sequences.
PROTEIN STRUCTURE PREDICTION
PHYRE2: Protein structure prediction.
PMP: Protein Model Portal.
I-TASSER: Protein structure & function predictions.
RaptorX: Web Portal for Protein Structure and Function Prediction.
GeneInfinity: List a complete collection of useful software and servers for many porpoises.
Pedro's BioMolecular Tools: Useful servers and links.
PROTEIN FLEXIBILITY PREDICTION
GlobPlot: Intrinsic Protein Disorder, Domain & Globularity Prediction.
DisEMBL: Intrinsic Protein Disorder Prediction.
ESpritz: Efficient disorder Prediction.
DisProt: Annotating protein sequences for intrinsically disorder regions from the literature..
SASB: Curated repository for small angle scattering data and models.
CALCULATION & ANALYSIS FROM 3D COORDINATES
Helix-Server: Volume, accessible surface areas, etc.
STAN: The STructure ANalysis server.
PSAP: A web based suite for protein structure analysis (Salt bridges, inter/intra molecular interactions, SS, etc.).
DALI: The Dali server is a network service for comparing protein structures in 3D.
PISA: Proteins, Interfaces, Structures and Assemblies
PDBeFOld: Structure Similarity (3D alignment).
BioInfo3D: Servers & Software
WAP: Water Analysis Package.
ProPKA: Web interface for pKa calculation.
- PDB2PQR Server: pKa calculations are performed by PROPKA.
PlayMolecule: Is a repository of best-in-kind applications regarding molecular predictors and tools for modelling.
- ProteinPrepare: for molecular dynamics simulations including protonation and H-optimization.
- BindScope: structure based protein-ligand binding predictor.
CASTp: It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
Caver: Is a software tool for analysis and visualization of tunnels and channels in protein structures.
V3 (Voss Volume Voxelator): Volume Calculation web tools.
MAP-CHANNELS: A computation tool to aid in the visualization and characterization of solvent channels.
EDTSurf: Quick and accurate construction of macromolecular surfaces .
Channel Mapping: provides straightforward visualization of pores and characterize the pores with metrics relevant for diffusion inside the crystals.
Click2Drug: Directory of computer-aided Drug Design tools.
AUTODOC: It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
ISOLDE:Your MD solution. ISOLDE is distributed as a plugin to UCSF ChimeraX.