Prediction Tools
ANTISOMA: ANTISOMA:
Reduction of the Aggregation Propensity of Monoclonal Antibodies.		 GNOMM:
Automated building of LPS-containing bacterial Outer Membranes for Molecular Dynamics simulations.		 GNOMM
GprotPRED: GprotPRED:
Detection of distinct Galpha families, Gbeta and Ggamma subunits of heterotrimeric G-proteins using profile Hidden Markov Models (pHMMs).		 MBPpred:
Prediction of Membrane lipid-Binding Proteins using profile Hidden Markov Models. 		MBPpred
HMMpTM: HMMpTM:
A Hidden Markov Model method for the topology prediction of alpha-helical transmembrane proteins that incorporates phosphorylation and glycosylation sites prediction.
CutProtFam-Pred:
A Cuticular Protein Family Prediction Tool
 CutProtFam-Pred:
AMYL-PRED AMYL-PRED:
A consensus prediction method for identifying possible amyloidogenic regions in protein sequences. 		AMYL-PRED 2:
A Consensus Method for Amyloid Propensity Prediction. 		AMYL-PRED 2
PRED-SIGNAL PRED-SIGNAL:
Prediction of signal peptides in archaea. 		PRED-LIPO:
Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model. 		cwpred
HMM-TM HMM-TM:
A Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information. 		CW-PRED:
Prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria		 cwpred
PRED-TMBB PRED-TMBB:
Predicting and discriminating beta-barrel outer membrane proteins with Hidden Markov Models		 PRED-COUPLE 2:
A tool that predicts the coupling specificity of G-protein coupled receptors to G-proteins		 pred-couple
PredSL:
PREDiction of Subcellular Location from the N-terminal Sequence		 PRED-COUPLE:
A method that implements refined profile Hidden Markov Models to predict the coupling specificity of G-protein coupled receptors to G-proteins		 pred-couple
ConBBPRED:
Consensus Prediction of TransMembrane Beta-Barrel Proteins		 PRED-GPCR:
GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models		 pred-gpcr
MCMBB:
Discrimination of beta-barrel outer membrane proteins with a Markov chain model		 waveTM:
Wavelet-based prediction of transmembrane segments in a-helical membrane proteins		 waveTM
predclass PRED-CLASS:
A system of cascading neural networks that classifies any protein, given its aminoacid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed		 CoPreTHi:
Combines the results of several methods that Predict Transmembrane regions in a joint prediction Histogram		 Cop_logo
orientm orienTM:
Topology Prediction of transmembrane proteins and segments		 PRED-TMR2:
PRED-TMR application with Neural Network preprocessing		 PRED-TMR2
PRED-TMR PRED-TMR:
Prediction of Transmembrane Segments in proteins based on statistical analysis		 SecStr:
Secondary Structure Prediction		 secstr
Biological Interaction Networks
The BLAD Interactome:
An interaction network of proteins related to Blood-cell targeting Autoimmune Diseases.
hGPCRnet:
An extended human GPCR interaction network, enabling the analysis of GPCR interactions combined with cell expression evidence.		 The Amyloid Interactome 2.0:
A protein-protein interaction network of amyloidogenic proteins and their experimentally verified interactors (Previous version: here).
Biological Databases
PerMemDB:
A database for eukaryotic peripheral membrane proteins
mpMoRFsDBlogo mpMoRFsDB:
A database of Molecular Recognition Features in Membrane Proteins		 AmyCo:
A freely available collection of amyloidoses and other clinical disorders related to amyloid deposition.
OMPdblogo OMPdb:
A database of ß-barrel outer membrane proteins from Gram-negative bacteria		 LepChorionDB:
Lepidoptera chorion protein database		 /LepChorionDB/
ExTopoDBlogo ExTopoDB:
A database of experimentally derived topological models of transmembrane proteins		 Human-gpDB:
A database of human GPCRs, G-proteins, Effectors and their interactions		 human_gpdb
cuticleDBlogo cuticleDB:
A relational database containing all structural proteins of Arthropod cuticle identified to date		 gpDB:
A database of G-proteins and their interaction with GPCRs		 gpDB
Applications for Sequence and Structure Analysis
hPATM hPATM:
Heuristic pairwise alignment for transmembrane proteins.
TMRPres2D TMRPres2D:
High quality visual representation of transmembrane protein models		 GeneVito:
Genome Visualization Tool		 GeneVito
non_red3 NON-RED:
A web tool to select biological sequences from a given set, with similarity/homology less than a user-defined level		 CAST:
Low-complexity region detection and selective masking		 cast
DAM-Bio DAM-Bio:
An integrated environment to support protein sequence and structure analysis		 FT:
Study of Residue Periodicities in Sequences		 FT