J.A. Gavira

Protein Crystallization & Crystallography

UGR CSIC LEC CSIC-UGR

Bioinformatic


There are in the web a good number of proteomics servers to predict from the isoelectric point to the 3D structure of a protein base on the aminoacid sequence and homology with other proteins.

EMBL-EBI: Bioinformatics services (several listed in this page).

ExPASy (Expert Protein Analysis System): Almost anything you need.


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.

GRAPHICS

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.

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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..

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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

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WAP: Water Analysis Package.

ProPKA: Web interface for pKa calculation.

PlayMolecule: Is a repository of best-in-kind applications regarding molecular predictors and tools for modelling.

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 .

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Channel Mapping: provides straightforward visualization of pores and characterize the pores with metrics relevant for diffusion inside the crystals.

DOCKING/Molecular Dynamics

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.

LigPlot: Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. (LigPlot+: NEW multiple ligand-protein interaction diagrams for drug discovery).


ISOLDE:Your MD solution. ISOLDE is distributed as a plugin to UCSF ChimeraX.