Prediction/analysis Tools for Sequences
	Multiple Sequence Alignment & Conserved Motifs Discovery[Sample Input and Sample Output (All with explanations!)]
	SPEM	Ref.[75]	Sequence, secondary structure Profiles Enhanced Multiple sequence alignment. (free download here.)
	SPEM-3D	Ref.[75]	Sequence, secondary structure Profiles Enhanced Multiple sequence alignment + 3D structures.
Prediction/analysis Tools for Secondary Structures
	Transmembrane helical topolgy [Sample Input and Sample Output (All with explanations!)]
	THUMBUP	Ref.[56]	Predicting transmembrane helical segments with burial propensity.
	THUMBUP-SP		Possible signal peptides are not excluded from prediction.
	UMDHMMTMHP	Ref.[56]	via Hidden Markov Model
	TUPS	Ref.[70]	Combination of THUMBUP, UMDHMMTMHP, and Phobius Signal peptide filter
	Structural Properties of proteins by Integrated NEural networks
	SPINE/Real-SPINE	Ref.[83-84]	Predict secondary structure, solvent accessibility (Real-value), psi torsion angle (Real-value) from a given sequence.
	Real-SPINE 2.0	Ref.[91]	Predict real-value torsion angles Psi and Phi from a given sequence.
	Real-SPINE 3.0	Ref.[96]	Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by fast guided-learning through a two-layer neural network
	SPINE-2D	Ref.[100]	Predict protein contact map
	SPINE XI	Ref.[104]	Improving real-value Phi/Psi prediction by combing two-state classifiers with real-value prediction
Prediction/analysis Tools for Tertiary Structures
	Fold recognition, alignment and structure prediction [Sample Input and Sample Output (All with explanations!)]
	SPARKS2	Ref.[59]	Knowledge-based energy score with sequence-profile and secondary structure information.
	SP3	Ref.[66]	Sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
	SP4	Ref.[85]	Fold Recognition by Concurrent Use of Solvent Accessibility and Residue Depth
	SP5	Ref.[94]	Improving protein fold recognition by using predicted torsion angles and profile-based gap penalty
	Decoy clustering
	SCUD	Ref.[71]	Fast Structure ClUstering of Decoys (DFIRE-minimized Helcal Decoys)
	The Domain Parser
	DDOMAIN	Ref.[86]	Fast structure-based domain prediction using a normalized domain-domain interaction profile
	Consensus Secondary Structure Assignment
	SKSP	Ref.[90]	Structure-based secondary-structure assignment based on the consensus over four independent methods.
Prediction/analysis Tools for Interactions
	Application of DFIRE energy function [See individual servers for sample input/output]
	DMONOMER	Ref.[52]	Scoring Protein structural monomer.
	DLOOP	Ref.[62]	Scoring loop conformations
	DMUTANT	Ref.[52]	Predicting mutation-induced change in stability
	DCOMPLEX	Ref.[61]	Protein-protein binding affinity and discrimination
	DDNA	Ref.[68]	Protein-DNA binding affinity and discrimination
	DDNA2	Ref.[102]	Protein-DNA binding affinity and discrimination 2
	Protein binding afinity and binding site prediction
	EMPIRE	Ref.[88]	Binding afinity prediction with an empirical scoring function and a simple reference state.
	PINUP	Ref.[81]	Binding site prediction with an empirical scoring function.
	ENDES	Ref.[98]	Enriching Near-native Docking-decoys Empricial Score (Download from downloads pages)
Prediction/analysis Tools for Network Graph
	Functional Module Prediction
	MC2	Ref.[80]	Module identifiCation by Merging Cliques.
	Protein Domain Graph Analysis Tools
	DOGMA	Ref.[67]	Webserver that allows on-line Analysis of plant domain graph.
Prediction/analysis Tools for Folding Kinetics
	Protein folding kinetics
	TCD	Ref.[44]	Folding rate prediction and TCD values
	Trans. State	Ref.[65]	Transition-state size prediction