1. Structure Annotation Tools
2. Structure Analysis
3. Domain Prediction, Globularity and Assembly Analysis
4. Hinge & Flexibility
5. Surface & Cavity Analysis
6. Binding Pocket and Binding Site Prediction
7. Ligand Interaction
8. Sites & Motifs
9. Interface Analysis
10. Contact Maps
11. Solvent Accessibility
12. Functional & Conserved Residues
13. Effects of Mutations
14. Disulphide Bonds
15. Metal Bindind Sites
SAS is a tool for applying structural information to a given
protein sequence. It uses FASTA to scan a given protein sequence against all
the proteins of known 3D structure in the Protein Data Bank (PDB). The
resultant multiple alignment can be coloured according to different structural
features and the matching 3D structures can be superimposed and viewed in
RasMol.
ESPript, Easy Sequencing in Postscript, is a utility to generate a
pretty PostScript output from aligned sequences.
SPICE is a browser for protein sequences, structures and their
annotations. It can display annotations for PDB, UniProt and Ensembl Peptides.
All data is retrieved from different sites on the Internet, that make their
annotations available using the DAS protocol. It is possible to add new
annotations to SPICE, and to compare them with the already available
information.
The Dali server is a network service for comparing protein
structures in 3D. Access also to related tools: SRS search for FSSP (families
of structurally similar proteins); search for DSSP; search for HSSP,
(homology-derived structures of proteins), a derived database merging
structural (2-D and 3-D) and sequence information (1-D).
PDBeMotif is an extremely fast and powerful search tool that
facilitates exploration of the Protein Data Bank (PDB) by combining protein
sequence, chemical structure and 3D data in a single search. Currently it is
the only tool that offers this kind of integration at this speed. PDBeMotif can
be used to examine the characteristics of the binding sites of single proteins
or classes of proteins such as Kinases and the conserved structural features of
their immediate environments either within the same specie or across different
species.
The WHAT IF Web Interface proposes a varied set of analyses on
protein structure.
Secondary
The ProFunc server had been developed to help identify the likely
biochemical function of a protein from its three-dimensional structure. It uses
both sequence- and structure-based methods (see below) to try to provide clues
as the the protein's likely or possible function. Often, where one method fails
to provide any functional insight another may be more helpful.
Protein Interactions Calculator (PIC) is a server which recognizes
various kinds of interactions;
PRIDE2 server calculates the PRobability of IDEntity between
three-dimensional domains (or whole structures) and offer varied various
compararisons with known structures (from fold identification, CATH and PDB
search, to NMR-NOE set comparison).
PBE server 2.0 aims to provide a platform for protein structure
The ConSurf server is a useful and user-friendly tool that enables
the identification of functionally important regions on the surface of a
protein or domain, of known three-dimensional (3D) structure, based on the
phylogenetic relations between its close sequence homologues.
StrucToolsn is a set of tools intended to provide a convenient web
interface to simple, commonly used structural biology calculations with PDB
files.
STING Millennium is a web based suite of programs that starts with
the visualization of a molecular structure and leads the user through a series
of operations resulting in an extensive structural analysis of the molecule
firestar server: predicting functional residues from structural
templates and alignment reliability
Evaluating the salt brIdges in proteins.
This program allows to analyse contacts between two chains or
within one chain in a given PDB file.
HORI - Higher Order Residue Interactions, is a web server to
compute higher order interactions (pairwise interaction, triplet interactions
and quadruple interactions) in a protein structure.
Identification of Stabilizing Residues in proteins.
MolTalk is a computational environment for doing Structural
Bioinformatics. At the base of i.Moltalk
FoldX provides a fast and quantitative estimation of the
importance of the interactions contributing to the stability of proteins and
protein complexes.
Web resource for the identification of sequence-structure links.
The resource consists of an exhaustive collection of annotated links between
the Swiss-Prot + TrEMBL sequence database entries and the PDB and SCOP
structure database entries.
iMolTalk is an interactive, Internet-based service for
computational analyses in Structural Biology that Compute Ramachandran plot
(?/? angles), Compute Distance Matrix of C? atoms, Find Contacts for a residue
or Distances between a pair of residues, Find Interface between two chains of a
structure, Compute Secondary structure assignment, Structural Alignment
Structural Alignment computation, derivation and verification. Structurally
compare all models in a structure, and Analyse Domain Motion Analyse domain
motion in homologous structures.
MaxSprout is a fast database algorithm for generating protein
backbone and side chain co-ordinates from a C(alpha) trace. The backbone is
assembled from fragments taken from known structures. Side chain conformations
are optimised in rotamer space using a rough potential energy function to avoid
clashes.
pDomain resource is centered around defining structural domains
from 3D coordinates. This resource brings together current state-of-the-art
algorithmic methods for partitioning proteins into domains.
Search for Conserved Domains within a protein sequence.
Dompred is a server designed to predict putative protein domains
and their boundaries for a given protein sequence. The server uses several
methods, from identifying obvious similarities to Pfam-A domain sequences to
predicting domains using DomSSEA in cases where sequence searching has yielded
no results.
The approach 'Protein Peeling' aims at cutting the 3D protein
structure into a limited set of 'Protein Units'. A more precise definition of
protein unit is a compact sub-region of the 3D structure corresponding to one
sequence fragment.
DOMpro is a web server to predict protein domain boundaries using
1D-Recursive Neural Networks and statistical methods.
DIAL is a web server for the automatic identification of
structural domains given the three-dimensional coordinates of a protein.
Intrinsic Protein Disorder, Domain & Globularity Prediction
PURE is a bioinformatics protocol to identify putative domains in
the Unassigned Regions.
Prediction of Protein Domains at University College Dublin.
Domain 3D is a method developed by Willie Taylor to identify
globular domains in protein structure.
DHcL (Domain Hierarchy and closed Loops)is a server for the
analysis of basic structural units of a protein. The server calculates domain
structures at different levels of energy hierarchy and elements of the
loop-n-lock structure, closed loops and van derWaals locks.
DynDom is a program to determine domains, hinge axes and hinge
bending residues in proteins where two conformations are available.
An Algorithm For Protein Hinge Prediction Using Elastic Network
Models
Analysis of Flexibility in Biomolecules and Networks.
Analysis of Flexibility in Biomolecules and Networks.
TLS Motion Determination (TLSMD) analyzes a protein crystal
structure for evidence of flexibility, e.g. local or inter-domain motions.
CAVER is a software tool for analysis and visualisation of
channels (tunnels) in protein structures. Channels are void pathways leading from
a cavity buried in a protein core to the surrounding solvent. Studying of these
pathways is highly important for drug design and molecular enzymology.
3D-SURFER is web-based software for protein surface comparison and
analysis. The server integrates various repertoire of methods to assist in high
throughput screening and visualization of protein surface comparisons. It takes
less than a second to perform an exhaustive comparison between a single protein
surface to all protein structures in the current PDB. Conveniently, the web
interface also renders animated protein rotations, displays CATH codes [Orengo
CA, Structure, 1997], and structure alignment calculations using the
Combinatorial Extension (CE) algorithm [Shindyalov IN and Bourne PE, Protein
Eng, 1998]
Accurate identification of channels in macromolecules.
SURF's_UP! is a web tool for analysis of functional relationships
in protein families as inferred from protein surface maps comparison. It
addresses a situation where only few members of the large homologous family are
characterized by experiment and function of others are unknown, either in a
general sense or in details (e.g. hydrolase with unknown specificity).
Molecular surface of proteins with the electrostatic potential is
a representation of protein three dimensional structures, which often gives
some clues to infer the function of proteins. eF-surf is a web server to
calculate the molecular surface of the up-loaded file with PDB format.
Binding sites and active sites of proteins and DNAs are often
associated with structural pockets and cavities. castP server uses the weighted
Delaunay triangulation and the alpha complex for shape measurements. It
provides identification and measurements of surface accessible pockets as well
as interior inaccessible cavities, for proteins and other molecules.
Protein Interactions Calculator (PIC) is a server which recognizes
various kinds of interactions;
HotPatch finds unusual patches on the surface of proteins, and
computes just how unusual they are (patch rareness), and how likely each patch
is to be of functional importance (functional confidence (FC).) The statistical
analysis is done by comparing your protein's surface against the surfaces of a
large set of proteins whose functional sites are known.
MolLoc takes in input two molecules and superimposes them on their
two most extended similar regions. This server can be used to test if two
molecules with different sequences and folds share any local surface
similarity.
Web tool for volume calculation.
IBIS is the NCBI Inferred Biomolecular Interactions Server. For a
given protein sequence or structure query, IBIS reports physical interactions
observed in experimentally-determined structures for this protein. IBIS also
infers/predicts interacting partners and binding sites by homology, by
inspecting the protein complexes formed by close homologs of a given query.
Pocket-Finder is a pocket detection algorithm based on Ligsite
written by Hendlich et al (1997). Pocket-Finder works by scanning a probe radius
1.6 angstoms along all gridlines of a grid resolution 0.9 angstroms surrounding
the protein.
FINDSITE is a threading-based binding site prediction/protein
functional inference/ligand screening algorithm that detects common ligand
binding sites in a set of evolutionarily related proteins. Crystal structures
as well as protein models can be used as the target structures.
LIGSITE is a web server for the automatic identification of
pockets on protein surface using the Connolly surface and the degree of
conservation!
PocketPicker - Binding Site Prediction
metaPocket is a meta server to identify pockets on protein surface
to predict ligand-binding sites!
castP server uses the weighted Delaunay triangulation and the
alpha complex for shape measurements. It provides identification and
measurements of surface accessible pockets as well as interior inaccessible
cavities, for proteins and other molecules.
3DLigandSite is an automated method for the prediction of ligand
binding sites.
Ligand Binding Site Prediction
Fast Prediction and Visualization of Protein Binding Pockets.
The MEDock (Maximum-Entropy based Docking) web server is aimed at
providing an efficient utility for prediction of ligand binding site.
Q-SiteFinder is a new method of ligand binding site prediction. It
works by binding hydrophobic (CH3) probes to the protein, and finding clusters
of probes with the most favourable binding energy. These clusters are placed in
rank order of the likelihood of being a binding site according to the sum total
binding energies for each cluster.
Protein binding site prediction with an empirical scoring
function.
Metal ion binding sites, affinities, and specificities from
structure
The aim of this server is to predict MHC Class-II binding regions
in an antigen sequence, using quantitative matrices.
STITCH is a resource to explore known and predicted interactions
of chemicals and proteins.
Ligand-Protein Contacts & Contacts of Structural Units.
PLATINUM is
Program for automatically plotting protein-ligand interactions.
The Catalytic Site Atlas (CSA) is a database documenting enzyme
active sites and catalytic residues in enzymes of 3D structure. We defined a
classification of catalytic residues which includes only those residues thought
to be directly involved in some aspect of the reaction catalysed by an enzyme.
SuMo allows you to screen the Protein Data Bank (PDB) for finding
ligand binding sites matching your protein structure or inversely, for finding
protein structures matching a given site in your protein. This method is
neither based on aminoacid sequence nor on fold comparisons.
All structures are reduced to matrices that contain just enough
information to define a fold, so the definition is general and large deviations
in coordinates are tolerated. A user supplies a matrix for a motif, and ProSMoS
lists all structures that exactly match this motif.
Multiple alignment of protein binding sites recognizes spatial
chemical binding patterns common to a Set of protein Structures.
SiteEngine recognizes regions on the surface of one protein that
resemble a specific binding site of another.
Patterns In Non-homologous Tertiary Structures. PINTS finds
similarities between protein structures consisting of amino acids that are
close in space, but not necessarily close or co-linear in sequence (local
structural patterns, for example the catalytic triad). Unlike other tools,
PINTS does not aim to find proteins adopting a similar fold.
FunClust is a web server for the identification of local
functional motifs in a set of non homologous protein structures
The LabelHash suite of programs and scripts can be used to match
point-based structural motifs to a set of target proteins. A motif is defined
by the C-alpha positions of a number of residues. Associated with each motif
point is a number of allowed residue labels.
RASMOT-3D PRO searches in protein structure files for proteins
possessing a group of residues in a topology similar to that adopted by a 3D
motif given in input.
Compare binding sites of proteins.
Given a set of motifs and a reference sequence, seeMotif helps to
visualize and exploring these motifs in appropriate structures selected based
on a reference sequence.
ProtMot, a PROTeins MOTif analysis tool. This web site analyzes
structure of proteins and output the list of hydrogen bonding patterns network
motifs. The list of motifs, a superset of the secondary structures, is shown
both projected on the protein structure and as a network motif significance
profile (SP), a chart which gives the occurrences of each motif in the protein.
PIPSA service is provided for the comparison of the electrostatic
interaction properties of proteins. It permits the classification of proteins
according to their interaction properties.
PDBePISA is an interactive tool for the exploration of
macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable
quaternary structures (assemblies), database searches of structurally similar
interfaces and assemblies, as well as searches on various assembly and PDB
entry parameters.
Multiple Alignment of Protein-Protein InterfaceS recognizes
spatially conserved chemical interactions shared by a set of protein-protein
interfaces.
Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting
protein binding sites.
The PROTORP server is a bioinformatics tool designed to analyse
the interfaces between protein chains in protein-protein associations.
A Macromolecular Interface Navigator. MolSurfer is a graphical
tool that links a 2D projection of a macromolecular interface to a 3D view of
the macromolecular structures. MolSurfer can be used to study protein-protein
and protein-DNA/RNA interfaces. The 2D projections of the computed interface
aid visualization of complicated interfacial geometries in 3D. Molecular
properties, including hydrophobicity and electrostatic potential, can be
projected onto the interface. MolSurfer can thereby aid exploration of
molecular complementarity, identification of binding 'hot spots' and prediction
of the effects of mutations. MolSurfer can also facilitate the location of
cavities at macromolecular interfaces.
A server for the analysis of the physicochemical features of
protein-protein interfaces.
AquaProt analyses protein-protein binding interface, defines
inter-residue interaction map within the interface and extracts related water
molecules.
VASCo is a program pipeline including a visualization tool to
calculate and visualize annotated surfaces with special emphasis on surface
contact regions and protein-protein interactions.
LIGPLOT Automatically generates schematic diagrams of
protein-ligand interactions for a given PDB file.
Ligand-Protein Contacts & Contacts of Structural Units
Scratch Protein Predictor metaserver.
Distill metaserver.
NNcon: Protein Contact Map Prediction Using Artificial Neural
Networks.
Contact Map Prediction
Solvent accessibility based Protein-Protein Interface
iDEntification and Recognition.
Accurate sequence-based prediction of relative Solvent
AccessiBiLitiEs, secondary structures and transmembrane domains for proteins of
unknown structure.
Calculation of Solvent Accessible Surface Areas, Atomic Solvation
Energies and Their Gradients for Macromolecules.
POPS is a fast algorithm to calculate solvent accessible surface
areas (SASAs) of proteins and nucleic acids at atomic (default) and residue
(coarse-grained) level.
ASAP predicts solvent accessible surface area of proteins.
This server provides graphical representation of solvent
accessibility of amino acid residues in proteins, with known structures.
The ConSurf server is a useful and user-friendly tool that enables
the identification of functionally important regions on the surface of a
protein or domain, of known three-dimensional (3D) structure, based on the
phylogenetic relations between its close sequence homologues.
Crescendo can only be used to identify residues that are
interacting with ligands or other proteins.
3dLOGO is a web server that allows the identification of 3D
locally conserved residues in a set of protein structures.
Firestar predicts functionally important residues from structural
templates and alignment reliability.
Prediction of Protein Stability Changes for Single-Site Mutations
from Sequences
FoldX provides a fast and quantitative estimation of the
importance of the interactions contributing to the stability of proteins and
protein complexes.
SIFT predicts whether an amino acid substitution affects protein
function based on sequence homology and the physical properties of amino acids.
SIFT can be applied to naturally occurring nonsynonymous polymorphisms and
laboratory-induced missense mutations.
Estimates the likelihood of a particular nonsynonymous (amino-acid
changing) coding SNP to cause a functional impact on the protein. It calculates
the subPSEC (substitution position-specific evolutionary conservation) score
based on an alignment of evolutionarily related proteins.
The server predicts the functional impact of amino-acid
substitutions in proteins, such as mutations discovered in cancer or missense
polymorphisms. The functional impact is assessed based on evolutionary
conservation of the affected amino acid in protein homologs.
CUPSAT is a tool to predict changes in protein stability upon
point mutations. The prediction model uses amino acid-atom potentials and
torsion angle distribution to assess the amino acid environment of the mutation
site. Additionally, the prediction model can distinguish the amino acid
environment using its solvent accessibility and secondary structure
specificity.
SNAP is a method for evaluating effects of single amino acid
substitutions on protein function. It was developed by Yana Bromberg in Rost
Lab, at Columbia University, New York.
Cysteines Disulfide Bonding State and Connectivity Predictor
DiANNA: unified software for Cysteine state and Disulfide Bond
partner prediction
Disulfide by Design is an application for the rational design of
disulfide bonds in proteins. For a given protein structural model, all residue
pairs are rapidly assessed for proximity and geometry consistent with disulfide
formation
Predicting the redox state of cysteins in proteins from multiple
sequence alignments
DSDBASE is a database on disulphide bonds in proteins that
provides information on native disulphides and those which are stereochemically
possible between pairs of residues in a protein.
MetalDetector predicts metal binding sites in proteins using
sequence information alone. Prediction is limited to transition metals (with
the addition of heme and Fe/S clusters) and to CYS and HIS as ligands.
This site uses the 'CHED' algorithm to predict 3D intra-chain
protein binding sites for transition metals (Zn, Fe, Mn, Cu, Ni, Co, and Ca and
Mg sites that can be replaced by a transition metal).
Acknowledgement: http://www.geneinfinity.org
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