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.
GeneInfinity: List a complete collection of useful software and servers for many porpoises.
Pedro's BioMolecular Tools: Useful servers and links.
PBE: Protein Structure Analysis and Comparison using Protein Blocks, a Structural Alphabet composed of 16 structural prototypes.
BioInfo3D: Servers & Software
ESPript: Easy Sequencing in PostScript, to render sequence similarities and secondary structure information from aligned sequences.
- RCrane: Allows for semi-automated building of RNA structure within Coot.
Deep View: Swiss-PdbViewer: is an visualization application allowing to analyze several proteins at the same time.
Chimera: is a visualization program that allows the visualization and analysis of molecular structures and related data i.e. density maps, assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
MolScript: For displaying molecular 3D structures in both schematic and detailed representations.
PDBsum: It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them. .
LigPlot+: Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file.
TopDraw: Is a sketchpad for drawing topology cartoons of proteins
Pro-Origami: Is a system for automatically generating protein structure cartoons.
3D Protein Structure & Kinemage Home Page: Is a scientific illustration presented as an interactive computer display with several development very useful tools for crystallography.
Multiple structure superposition
3D-SS: 3-Dimensional structural superposition.
MATRAS: Protein 3D Structure Comparison.
SuperPose: Protein superposition server.
MultiProt: It finds the common geometrical cores between the input molecules.
PDBeFold: Structure Similarity.
PROTEIN STRUCTURE PREDICTION
PHYRE2: Protein structure prediction.
I-TASSER: Protein structure & function predictions.
RaptorX: Web Portal for Protein Structure and Function Prediction.
SWISS-MODEL: Protein structure prediction.
CAMEO: Continuous Automatic Model Evaluation.
ModelArchive: Since 2006 theoretical models are no longer allowed at PDB. Here are easily identificable (DOIs) curated models.
AlphaFold2: Protein structure prediction using multiple sequence alignments generated through an MMseqs2n.
AlphaFold Colab: Easily predict the structure of a protein using a slightly simplified version of AlphaFold v2.1.0.
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..
CALCULATION & ANALYSIS FROM 3D COORDINATES
WHATIF: Web Interface proposes a varied set of analyses on protein structure.
VADAR: Single (or Multiple) Model Protein Structure Analysis
PIC: Protein Interactions Calculator. Web based suite for protein structure analysis: salt bridges, inter/intra molecular interactions, etc.
PSAP: A web based suite for protein structure analysis.
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).
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.