Structure Related Sites

Protein/Nucleic Acid Structure Search Sites

3D_ali is a database of aligned protein structures and related sequences at EMBL-heidelberg (Updated 5/1/99).

3DB-browser (obselete)

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). The relationships among structure, function and property are visualized by 3DinSight: e.g., real-time 3D images displaying structures with automatically mapped functional sites; and graph plots integrating amino acid property vs. sequence, structural and functional information. 3DinSight has also various links to other databases and provides several convenient interfaces. For more detail about 3DinSight, please see here (Updated 6/16/2).

AGDIR An algorithm to predict the helical content of
peptides at EMBL-heidelberg (Updated 5/1/99)

Aqua server server can be used to determine the Completeness of NOE distance restraints and Redundancy of intra-residual NOE distance restraints at EMBL-heidelberg (Updated 5/1/99)

ASC - Analytic Surface Calculation of PDB Protein Structures at EMBL-heidelberg on the Homepage of Frank Eisenhaber. (Updated 4/8/99)

ASTRAL compendium provides databases and tools useful for analyzing protein structures and their sequences. It is partially derived from, and augments the SCOP: Structural Classification of Proteins database. Most of the resources provided here depend upon the coordinate files maintained and distributed by the Protein Data Bank.

The BindingDB is a public, web-accessible database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds.The database currently contains data generated by isothermal titration calorimetry (ITC) and enzyme inhibition (Enz. Inhib.) methods; other techniques will be included in the future (Updated 6/16/2).

BioMagResBank is a database of NMR-derived protein structures, developed and maintained by the University of Wisconsin at Madison, but is also available at NIH (Updated 5/1/99).

Chirality Database: Chiral World

provides a group of databases in H1 NMR, C13 NMR, and CD/UV, which should be useful for organic chemists and biochemists (Updated 3/25/01).

Contacts of Structural Units (CSU software)

Analysis of interatomic contacts in PDB entries that you can submit. Alternatively, you can access it here. (Updated 10/03/01)

COMPARER ON-LINE

This form creates a COMPARER alignment output file in the JOY format. Protein structure superposition uses the DiCE structural alignment program (unpublished). For a local version of this server using the STAMP alignment program go here. Comparer output files are also available. Enter the PDB code of the proteins to be aligned or choose a file, together with the chain identifier and residue numbers (Updated 10/3/01).

Culling the PDB by Resolution and Sequence Identity

- For many applications in protein structure analysis, it is necessary to have a list of chains from the Protein Databank (PDB) such that no two chains in the list have a sequence identity above some threshold and all chains in the list have a resolution better than or equal to some value. The site is maintained by the Fox Chase Cancer Center (Updated 10/3/01).

Dali- Comparison of protein structures in 3D (at EBI). It is equivalent to a multiple sequence alignment except it is with structure ( server down 5/22/99 )(Updated 5/1/99).

DSSP - Database of Secondary Structure of Proteins from PDB at EMBL, Heidelberg (Updated 5/2/99)

Documentation

Electron Density Server at Uppsala University The information on this server is based on the Protein Data Bank entries and deposited structure factors. This server is a prototype version. The electron density maps derived from the structure factors and coordinates are generated using an automatic script, using the programs CNS or CCP4. Beware of maps for which the calculated R factor is high. This may indicate a problem during the parsing of the structure factor or coordinate files. The site is maintained at BMC Molecular Biology Server at Uppsala University (Updated 3/25/01).

Enzyme Data Bank contains the recommended name, catalytic activity, etc. for each type of characterized enzyme for which an EC number has been provided at the Maize Genome Database (5/22/99)

HEAVY-ATOM DATABANK have collected information on the preparation and characterisation of HEAVY-ATOM derivatives of protein crystals (8/31/99).

HIC-Up, the Hetero-compound Information Centre

- Uppsala, a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds ("small molecules") (Updated 10/03/01).

HSSP is a Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL, Heidelberg (Updated 5/2/99).

Image Library of Biological Molecules

offers information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It is maintained at the Institute of Molecular Biotechnology (Updated 8/23/99).

Hetero Components Database

Isoelectric Point Service- a program that calculates the pI from a given amino acid sequence at EMBL, Heidelberg (Updated 5/2/99).

JOY server

is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and help understand the conservation of amino acids in their specific local environments. For instance, it has been recognised that a sidechain hydrogen-bonded to a main-chain amide plays an important role in stabilizing the 3D structure and is generally well conserved during evolution. You can access the main page by clicking here (Updated 10/03/01).

Ligand-Protein Contacts (LPC software)

Analysis of interatomic contacts in Ligand-Protein complexes, which allows you to submit the PDB letter code. Alternatively, you can access it here. (Updated 10/3/01)

Metal Containing Biopolymer Structures is a database of metal containing biopolymers at the image library of biological molecules IMB (Updated 3/25/01).

Molecular Movements Database

This database describes the motions that occur in proteins and other macromolecules (such as RNA). Associated with it are a variety of free software tools for structural analysis (Updated 3/25/01).

Molsurfer provides 2D maps to navigate 3D structures of proteins at EMBL-heidelberg (Updated 5/1/99).

Morphing Server and Database-

This server will produce 2D and 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations. The website is maintained at the Gerstein Bioinformatics Lab at Yale University (Updated 5/13/01).

MutaProt provides 1) a full list of file-pairs which differ by one, or two, amino acids; 2) Amino acid neighbors, and atomic contacts, of the mutated residue(s) (based on CSU software); 3) 3D Visualization of the mutated region(s) (using CHIME, click to install) (Updated 10/03/01).

NIMH Psychoactive Drug Screening Program Drug Database

An interactive database of Ki values for a large number of psychoactive compounds at a large number of neurotransmitter receptors, channels and transporters. This is part of the NIMH Psychoactive Drug Screening Program (Updated 10/17/99).

OCA

has all the power and functionality of 3DB Browser and more. It provides a more informative way to search the PDB database. (Updated 2/12/00).

PDB Cull Lists This site maintains a weekly update of cull lists of protein chains from the Protein Database (PDB) (Updated 9/23/99).

PDB Lite:

Search for 3D structures of proteins, DNA, RNA in an interface designed for novices or occasional-user scientists or educators. Detailed help on how to save a PDB file to disk for use with RasMol or Protein Explorer (Updated 8/20/00).

Name	Location	Comments
PDB Lite	ANGIS	NA
PDB Lite	Weizmann Institute	NA
PDB Lite	Tel Aviv University	NA
PDB Lite	Cambridge Univ.	NA
PDB Lite	Boston University	NA

PDB Lite is also available (old version without direct links to Protein Explorer) updated weekly with new entries from RCSB.

Name	Location	Comments
PDB Lite	The Walter Eliza Institute of Medical Research	NA
PDB Lite	Birkbeck University of London	NA

PDB Search/Gateway

Name	Location	Comments
PDB Search	RSCB	this is the one that is directed by the old server http://www.pdb.bnl.gov
PDB Search	Rutgers	this site is maintained at Rutgers, a state University of New Jersey.
PDB Search	NIST	NA

PDB molecular weight search tool

is a useful tool for finding a protein within a molecular weight range. The site is maintained at the Bioinformatics Genome FTP server (Updated 3/25/01).

PDB to MultiGif Page

takes the 3D structure and generates an animated image which can be displayed using any browser (Updated 10/17/99).

Predator does Protein secondary structure prediction from
multiple sequences at EMBL-heidelberg (Updated 5/1/99).

Protein Mutant Database (PMD) is a mutant database of proteins would be valuable as a basis of protein engineering. Our database is of a type based on literature (not on proteins); that is, each entry of the database corresponds to one article which describes protein mutations (Updated 10/03/01).

Protein Predict provides a variety of useful services at EMBL-heidelberg (Updated 5/1/99).

Note: On 5/1/99, I had some trouble connecting.

Protein Sequence Search Tool-

has a wide range of tools for analyzing the sequence of proteins found in the PDB database. The site is maintained at the Bioinformatics Genome FTP server (Updated 3/25/01).

Protherm contains numerical data of several thermodynamic parameters, namely, Gibbs free energy, enthalpy, heat capacity, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins upon mutations (Updated 10/03/01).

PROWL - a resource for protein chemistry and mass spectrometry; Useful information about synthetic peptides at the department of Biochemistry, Structural Biology & Chemistry at The Rockefeller University (Updated 4/6/99).

SAPS - Statistical Analysis of Protein Sequences (Updated 4/4/99)

SRS - Sequence Retrieval System at EMBL-heidelberg allows the user to compare the major structural and sequence databases of the world.

SSCP Secondary structural content prediction from
amino acid composition at EMBL-heidelberg (5/1/99).

Stride is a Knowledge - based protein secondary structure
assignment from atomic coordinates at EMBL-heidelberg (5/1/99).

TIM-DB TIM-DB provides a complete and updated view of all TIM barrel domains in PDB structures. TIM-DB is updated weekly (after PDB releases the new entries on Wednesday morning) and is therefore more suitable for researchers interested in TIM barrel proteins than the more general SCOP and CATH databases. The TIM barrel proteins are classified in TIM-DB according to their EC code. Historically, this is the most usual way in which TIM barrel domains have been classified. From the main page of this web site, all the PDB structures can be accessed following the corresponding enzyme activity link. The consistency of TIM-DB with SCOP and CATH is frequently checked (Updated 2/12/00).

TMpred - Prediction of Transmembrane Regions and Orientation (Updated 4/4/99)

VAST Search

Virus Structure Resource server provides images of virus structures determined by a group in the Structural Biology Programme at EMBL-heidelberg (5/1/99).

WHAT IF (web interface) (platform independent; Free) provides nearly 2000 options in fields as diverse as
homology modeling, drug docking, electrostatics calculations, structure validation and visualisation (Updated 10/03/01).