There are a good number of proteomics servers to predict from the isoelectric point to the 3D structural model 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.

• 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.

HotspotWizard: Design of mutations & more.

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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.

PBE: Protein Structure Analysis and Comparison using Protein Blocks, a Structural Alphabet composed of 16 structural prototypes.

BioInfo3D: Servers & Software

Jcat: (Java) Codon Adaptation Tool.

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FIREPROT: Fully automated ancestral sequence reconstruction

Consensus Finder: Fully automated consensus sequence reconstruction

GRAPHICS

ESPript: Easy Sequencing in PostScript, to render sequence similarities and secondary structure information from aligned sequences.

Coot: Macromolecular model building, model completion and validation. (CCP4wiki-COOT: Instalation, scripts, etc.)

• RCrane: Allows for semi-automated building of RNA structure within Coot.

PyMOL: Is a molecular visualization system. (Pymol-wiki)

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.

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SciDRAW: Search what you may need...

BioIcons

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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

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.

AlphaFill: AlphaFold models enriched with ligands and co-factors

Robetta/RoseTTAFold: A a protein structure prediction service that is continually evaluated through CAMEO.

AlphaFold3: AF3 Server can generate highly accurate biomolecular structure predictions containing proteins, DNA, RNA, ligands, ions, etc

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PHYRE2: Protein structure prediction.

I-TASSER: Protein structure & function predictions.

RaptorX: Web Portal for Protein Structure and Function Prediction.

SWISS-MODEL: Protein structure prediction.

HawkDock: A web server for the structural prediction and analysis of protein-protein complex.

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CAMEO: Continuous Automatic Model Evaluation.

ModelArchive: Since 2006 theoretical models are no longer allowed at PDB. Here are easily identificable (DOIs) curated models.

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.

• DALI_old

PISA: Proteins, Interfaces, Structures and Assemblies

PDBeFOld: Structure Similarity (3D alignment).

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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.
• etc.

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.

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

CheckMyBlob: Identify & Validate your ligands.

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