Protein Tertiary Structure
Databases & classification
Protein Data Bank. The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
www.rcsb.org
CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
http://www.cathdb.info/
3DinSight is an integrated database and search tool for structure, property and function of biomolecules, which will help researchers to get insight into their relationship. The structural data, functional data (motifs, mutations, protein-nucleic acid binding, protein-ligand binding etc.) and property data (amino acid property and thermodynamic data of proteins) of biomolecules are implemented into a relational database, so that flexible searches can be done by a combination of queries (SQL).
http://gibk26.bse.kyutech.ac.jp/jouhou/3dinsight/3DinSight.html
NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models.
http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml
The Dali Database is based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank* (PDB).
http://ekhidna.biocenter.helsinki.fi/dali/start
A database of three-dimensional protein models calculated by comparative modeling.
http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
The Conserved Domain Database (CDD) contains protein domain models imported from outside sources, such as Pfam and SMART, and curated at NCBI.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources.
http://gene3d.biochem.ucl.ac.uk/Gene3D/
ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins.
http://gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html
Thermodynamic database for protein-nucleic acid interactions. ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids.
http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
Protein-Nucleic Acid Complex Database is a database containing structural data of protein-nucleic acid complex. These data are classified according to recognition motif of proteins and DNA forms involved in the complex.
http://gibk26.bse.kyutech.ac.jp/jouhou/3dinsight/complexdb.html
Nucleic Acid Database, a repository of three-dimensional structural information about nucleic acids.
http://ndbserver.rutgers.edu/
The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
http://swissmodel.expasy.org/repository/
Search & retrieval
Online text-based search and retrieval system used at NCBI for finding structures by keywords, id number, database number, etc.
http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure
3D Domains are compact structural domains identified automatically in Entrez's macromolecular three-dimensional structure database.
http://www.ncbi.nlm.nih.gov/sites/entrez?db=domains
VAST Search is NCBI's structure-structure similarity search service. It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database. VAST Search computes a list of structure neighbors that you may browse interactively, viewing superpositions and alignments by molecular graphics.
http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html
ProteinDBS is the first real-time search engine for retrieving similar protein tertiary structures in Protein Data Bank (PDB). This system provides two types of query method: query by PDB protein chain ID and by 3D coordinates of newly-discovered proteins in PDB format. With computational techniques, similar protein structures with ranked order will be returned to users in seconds. Our database proteins are weekly updated to be consistent with PDB database.
http://proteindbs.rnet.missouri.edu/
Structure analysis
The SCOP (Structural Classification of Proteins) database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
http://scop.mrc-lmb.cam.ac.uk/scop/
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).
http://www.ebi.ac.uk/dali/
iMolTalk is an interactive, Internet-based service for computational analyses in Structural Biology that Compute Ramachandran plot (Φ/Ψ angles), Compute Distance Matrix of Cα 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.
http://i.moltalk.org/
MolTalk is a computational environment for doing Structural Bioinformatics. At the base of i.Moltalk
http://www.moltalk.org/
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.
http://www.russell.embl.de/pints/
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
http://luna.bioc.columbia.edu/SMS/sms.html
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
http://foldx.crg.es/
The SSAP server allows users to compare the structures of two proteins and view the subsequent structural alignment. To use this server you will need to specify either an existing PDB code/CATH domain (left box) or the full path to a local PDB file (right box) for each structure.
http://www.cathdb.info/cgi-bin/cath/SsapServer.pl
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.
http://www.ebi.ac.uk/maxsprout/
Secondary Structure Matching (SSM) is an interactive service for comparing protein structures in 3D. The service provides for:
- multiple comparison and 3D alignment of protein structures
- pairwise comparison and 3D alignment of protein structures
- examination of a protein structure for similarity with the whole PDB or SCOP archives
- best Ca-alignment of compared structures
http://www.ebi.ac.uk/msd-srv/ssm/
Integrated search for small structure motifs, including non-peptidic structures.
http://www.ebi.ac.uk/msd-srv/msdmotif/index.jsp
The WHAT IF Web Interface proposes a varied set of analyses on protein structure.
http://swift.cmbi.ru.nl/servers/html/index.html
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.
http://projects.villa-bosch.de/dbase/molsurfer/
PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. Provide PDB search through sequence match.
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
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.
http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/
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.
http://www.efamily.org.uk/software/dasclients/spice/
TLS Motion Determination (TLSMD) analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.
http://skuld.bmsc.washington.edu/~tlsmd/index.html
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.
http://surface.bio.uniroma2.it/seq2struct/
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
http://consurf.tau.ac.il/
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.
http://hotpatch.mbi.ucla.edu/
SURFACE is a database containing the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-derived information about function or interaction abilities.
http://cbm.bio.uniroma2.it/surface/
RosettaDesign identifies low energy sequences for specified protein backbones, and has been used previously to stabilize proteins and create new protein structures.
http://rosettadesign.med.unc.edu/index.html
Structure prediction
Predictor@home is a world-community experiment and effort to use distributed world-wide-web volunteer resources to assemble a supercomputer able to predict protein structure from protein sequence(note: this is not a resource) .
http://predictor.chem.lsa.umich.edu/
Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. In addition to support of the CASP meetings our goal is to promote an evaluation of prediction methods on a continuing basis (note: not a resource).
http://predictioncenter.gc.ucdavis.edu/
The Structure Prediction Meta Server provides access to various fold recognition, function prediction and local structure prediction methods.
http://meta.bioinfo.pl/submit_wizard.pl
The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice (secondary structure, fold, transmembrane topology).
http://bioinf.cs.ucl.ac.uk/psipred/
A computational tool for predicting disorder in proteins. DisEMBL is useful for target selection and the design of constructs as needed for many biochemical studies, particularly structural biology and structural genomics initiatives.
http://dis.embl.de/
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.
http://swissmodel.expasy.org/
3D-JIGSAW builds three-dimensional models for proteins based on homologues of known structure
http://www.bmm.icnet.uk/servers/3djigsaw/
ESyPred3D is a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy using neural networks.
http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/
A Fast, Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information -use Phyre instead.
http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html
FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure.
http://www-cryst.bioc.cam.ac.uk/~fugue
Homology detection & structure prediction by HMM-HMM comparison
http://toolkit.tuebingen.mpg.de/hhpred
LOOPP is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure. The signals we are using include straightforward sequence alignment, sequence profile, threading, secondary structure and exposed surface area prediction.
http://cbsuapps.tc.cornell.edu/loopp.aspx
HMM-based Protein Structure Prediction
http://www.soe.ucsc.edu/research/compbio/HMM-apps/T02-query.html
HMM-based Protein Structure Prediction
http://www.soe.ucsc.edu/research/compbio/SAM_T06/T06-query.html
Threading is one of the very few methods available which can predict the fold for a protein in the absence of an evolutionary relationship, though if there is an evolutionary link between the target protein and a protein of known structure then there are better methods available
http://bioinf.cs.ucl.ac.uk/threader/threader.html
The HMMSTR/Rosetta Server predicts the structure of proteins from the sequence : secondary, local, supersecondary, and tertiary.
http://bioinf.cs.ucl.ac.uk/threader/threader.html
The nFOLD3 protein fold recognition server allows you to generate 3D models of a protein from its amino acid sequence.
http://www.reading.ac.uk/bioinf/nFOLD/
Your sequence will be aligned to about 10348 PDB template structures. The alignments will be ranked and the results mailed back to you. By default, the 50 top ranked proteins will be listed and the top 10 alignments printed out. Models will be built for 5 proteins.
http://www.zbh.uni-hamburg.de/wurst/
FORTE: a profile-profile comparison tool for protein fold recognition.
http://www.cbrc.jp/htbin/forte-cgi/forte_form.pl
Fold-recognition services based on Sequence-Derived Properties, combining old and new methods.
http://inub.cse.buffalo.edu/
AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html
ESyPred3D is a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy using neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER.
http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/
Online Protein Structural Prediction Pipeline
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGE
FoldIndex© tries to answer to the question: Will this protein fold?
http://bip.weizmann.ac.il/fldbin/findex
Structure alignment
MAMMOTH (Matching Molecular Models Obtained from Theory) is a sequence-independent protein structural alignment method. It allows the comparison of an experimental protein structure with an arbitrary low-resolution protein tertiary model. It also allows the comparison of two experimental structures, or the search for similar structures to a query structure in a database.
http://ub.cbm.uam.es/servers/mammoth/mammoth.php
Translate sequence - structure alignment (AL) into tertiary structure (TS)
http://predictioncenter.org/local/al2ts/al2ts.html
Protein Structure Alignments by TOPOFIT : A structural alignment of proteins by a superimposition of common volumes at a topomax point. Online serevr and database.
http://mozart.bio.neu.edu/topofit/index.php
The SISYPHUS database contains a collection of manually curated structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins.
http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/
Databases and Tools for 3-D Protein Structure Comparison and Alignment
http://cl.sdsc.edu/ce.html
HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER.
http://www-cryst.bioc.cam.ac.uk/homstrad/
3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several three-dimensional protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures.
http://cluster.physics.iisc.ernet.in/3dss/index.shtml
Effects of mutations
Prediction of Protein Stability Changes for Single-Site Mutations from Sequences
http://www.ics.uci.edu/%7Ebaldig/mutation.html
FOLD-X is a program for calculating the folding pathways of proteins and for calculating the effect of a point mutation on the stability of a protein.
http://fold-x.embl-heidelberg.de:1100/cgi-bin/main.cgi
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.
http://blocks.fhcrc.org/sift/SIFT.html
Conserved Residues
3dLOGO is a web server that allows the identification of 3D locally conserved residues in a set of protein structures.
http://3dlogo.uniroma2.it/3dLOGO/index.html