Zhou Lab Services

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 X Refs.[103,107] Improving real-value Phi/Psi prediction by combing two-state classifiers with real-value prediction
SPINE D Refs.[118] Predicting short and long disordered regions in proteins
Prediction/analysis Tools for Tertiary Structures
Fold recognition, alignment and structure prediction [Sample Input and Sample Output (All with explanations!)]
SPARKS-X Ref.[114] The newest version of protein fold recognition.
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.
SPalign Ref.[120] Size-independent pairwise structural alignment
Prediction/analysis Tools for Interactions
Application of DFIRE energy function [See individual servers for sample input/output]
dDFIRE/DFIRE 2.0 Ref.[92] Scoring Protein Conformational Free Energy
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
DDNA3 Ref.[105] Protein-DNA binding affinity and discrimination 3
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)
SPOT Ref.[105] Structure-based prediction of DNA-binding proteins.
SPOT-Struc(RNA) Ref.[109] Structure-based prediction of RNA-binding proteins.
SPOT-Seq(RNA) Ref.[115] Sequence-based prediction of RNA-binding proteins.
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

Copyright (c) 2005-2007, IUPUI, IN.
Credit: The background for SCUD image and logo in EMPIRE image were from google image.