Israel Science and Technology Directory

Biomedical Software

Online Software for Protein Sequence and Structure Analysis
Online ToolDescription
CASTpComputed atlas of surface topography of proteins.
ClustalW2Multiple Sequence Alignment for DNA or proteins.
DynDomDynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
ExPASy COILSProgram that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score.
GCUA - Graphical Codon Usage AnalyserUsage of each codon in the sequence will be plotted against the fraction of usage of the codon in the selected organism.
GalaxyWEBA web server for protein structure prediction, refinement, and related methods.
I-TASSERIterative Threading ASSEmbly Refinement is a hierarchical approach to protein structure and function prediction.
IUPredIUPred3 is a combined web interface that allows to identify disordered protein regions using IUPred2 and disordered binding regions using ANCHOR2.
JVirGelCreate your own Virtual 2D Protein Gel
Mol* 3D ViewerProtein Feature Viewer provides graphical summaries of PDB protein biological and structural features and their relationships with UniProtKB entries
Motif ScanSearches for all known motifs that occur in a sequence.
NetOGlycNeural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
PI2PEProtein Interface/Interface Prediction Engine
PROMPTCompare protein sets for features like molecular weight, isoelectric point, enzyme classifications or structural classes.
PROVEANProtein Variation Effect Analyzer - A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
PSIPREDProtein Sequence Analysis Workbench of secondary structure prediction methods.
Patch FinderFind and display the largest positive electrostatic patch on a protein surface.
Phyre2Protein Homology/analogY Recognition Engine - Protein structure prediction
PolyPhen-2Polymorphism Phenotyping tool that predicts possible impact of an amino acid substitution on the structure and function of a human protein.
ProSA-webInteractive web service for the recognition of errors in three-dimensional structures of proteins.
ProtParamCalculates amino acid composition, theoretical pI, molecular weight.
Protein DigestFor a given protein sequence presents lists of peptides that would be produced using Trypsin, chymotrypsin, elastase, cyanogen bromide, iodosobenzoate etc.
QuasiMotiFinderA server for the identification of signatures and signature-like patterns in protein sequences.
SWISS-MODELAn Automated Comparative Protein Modeling Server.
TM-alignStructural alignment program for comparing two proteins.
VADARVADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data.