Israel Science and Technology Directory

Biomedical : Online Software for Protein Sequence and Structure Analysis

Online ToolDescription
APSSP2Advanced Protein Secondary Structure Prediction Server
Block MakerFinds conserved blocks in a group of two or more unaligned protein sequences.
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.
ERRATA program for verification of protein structures based on patterns of nonbonded atomic interactions.
ExPASy Proteomics ToolsDiverse utilities for protein identification and characterization.
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.
Motif ScanSearches for all known motifs that occur in a sequence.
NetOGlycNeural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
PDB GoodiesInput PDB file. Output includes amino acid composition, molecular weight, volume, bond lengths, bond angles, and torsion angles. Change the residues to poly-Ala. Remove HETATM(s) present in the PDB file.
PI2PEProtein Interface/Interface Prediction Engine
PROMPTCompare protein sets for features like molecular weight, isoelectric point, enzyme classifications or structural classes.
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.
SIFTSIFT predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related 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.