• Tertiary structure
  
• Secondary structure
  
• Cristallography
  
• NMR data analysis
  

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Tertiary structure

	Name	Description	Link
	3D structures superimposition (NPS@)
	ATOME	@utomatic Threading Optimisation Modelling & Evaluation	@TOME server
	AutoDock	Automated Docking of Flexible Ligands to Receptors	website
	CaspR	An automated approach for molecular replacement	homepage
	COSA	Clustal ouput structural analysis	online form
	COUDES	web server for beta-turn prediction	COUDES online
	ElNémo	The Web-interface to The Elastic Network Model, a fast and simple tool to compute the low frequency normal modes of a protein.	homepage
	ESAP	Prediction of protein loop conformation	webpage
	Geno3D	Automatic molecular modeling	online form
	HMMTOP	an automatic server for predicting transmembrane helices and topology of proteins	website
	IMGT/StructuralQuery	Retrieval of IMGT/3Dstructure-DB entries using domain type and/or position structural criteria	online form
	KinDOCK	Ligand Transposition Server	KinDOCK server
	LocPred	Local structure prediction	LocPred online
	PAT (Protein Analysis Toolkit)	toolkit to facilitate the combination of different processing tools for more complex protein analyses	PAT server
	PPG	Protein Picture Generator	PPG online
	SA-Search	search for 3D fragments similar to (fragments of) a query structure	SA-Search online
	SCit	Tools for protein side chain conformation analysis and editing	SCit online
	Small compounds	project involving the screening of databases of small chemical compounds	Project homepage
	SuMo	Surfing the Molecules - Search for similar 3D sites in proteins	homepage
	TMHMM	Prediction of transmembrane helices in proteins	TMHMM server
	WLoop	predict protein loop backbone structures from their sequences and their flank backbone structures	WLoop online
	XmMol	desktop macromolecular visualization and modeling tool	homepage

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Secondary structure

	Name	Description	Link
	Dicroprot	a single package most of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments	homepage
	DSC	Discrimination of protein Secondary structure Class
	DSSP	Discrimination of protein Secondary structure Class
	Gor IV	method for predicting protein secondary structure from amino acid sequence	webpage
	HCA	Hydrophobic cluster analysis	HCA online
	NNSSP	Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignment
	PAT (Protein Analysis Toolkit)	toolkit to facilitate the combination of different processing tools for more complex protein analyses	PAT server
	PREDATOR	Protein secondary structure prediction from a single sequence or a set of sequences
	PSIPRED	a simple and reliable secondary structure prediction method	PSIPRED homepage
	Secondary structure prediction		toolkit
	SIMPA	protein secundary structure prediction based on the "nearest-neighbor" notion	webpage
	STRIDE	Definition of secondary structure of proteins given a set of 3D coordinates
	TopPred2	Topology prediction of membrane proteins

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Cristallography

	Name	Description	Link
	SAmBA	Interactively computes the experimental protocol corresponding to your combination of variables and states	SAmBA online

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NMR data analysis

	Name	Description	Link
	CINDY	Graphical NMR assignment software
	CROWD	Noe intensity simulation software
	GIFA	an NMR processing program which includes many signal processing methods, such as Maximum Entropy, Linear Prediction, automatic Phasing, line fiting, base line correction...
	RESCUE	An artificial neural network tool for the NMR spectral assignment of proteins

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