Internet Resources

 
Bioinformatics & Genomics


 
Protein Structure



 
3-D Structure Prediction



 
Protein Data Bank (PDB)



 
Searches of PDB



 
Secondary Structure Prediction & Assignment



 
Structure Analysis



 
Structure Comparison



 
Structure Databases



 
Transmembrane Prediction

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123D+
[National Institutes of Health] 123D+ is a program that combines sequence profiles, secondary structure prediction, and contact capacity potentials to thread a protein
sequence through the set of structures.

[more info][10493]

Biosciences and Biotechnology at LLNL
[Lawrence Livermore National Laboratory (LLNL)] “Working with academia, industry, and government, we leverage the laboratory’s capabilities in the physical and engineering sciences to conduct biosciences and biotechnology research of national importance.” This site contains information about LLNL’s bioscience research which includes three main areas: genomics, disease susceptibility and prevention, and healthcare and medical device technology.

[more info][12511]

Calculate Spheres
[Weizmann Institute] This program uses the Ligand-Protein Contacts (LPC) software, which analyzes the interatomic contacts in ligand-protein complexes, and the Contacts of Structural Units (CSU) software, which analyzes interatomic contacts in PDB entries, to display a ligand and its binding site.

[more info][12255]

Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.


[more info][12374]

EF-Hand Calcium-Binding Proteins Data Library
[Vanderbilt University] The EF-Hand Calcium-Binding Proteins Data Library is a growing collection of published sequence, structural, functional, and other
information about EF-hand calcium-binding proteins and their roles in cellular signal transduction.

[more info][13790]

ERRAT
[UCLA] A protein structure verification algorithm that analyzes the statistics of non-bonded interactions between different atom types.

[more info][10499]

Ligand-Protein Contacts & Contacts of Structural Units
[Weizmann Institute] LPC analyzes the interatomic contacts in ligand-protein complexes, and CSU analyzes the interatomic contacts in PDB protein entries.

[more info][12254]

MatrixPlot
[Technical University of Denmark] MatrixPlot can be used to generate mutual information plots of sequence alignments, distance matrices of sequences with known 3D
coordinates, and plots of user provided matrix files. Both protein and nucleic acid sequences can be analyzed.

[more info][12403]

Merohedral Crystal Twinning Server
[UCLA-DOE] Twinning is a crystal growth disorder in which the specimen is composed of distinct domains
whose orientations differ but are related in a particular, well-defined way. Twinning usually prevents a successful structure determination unless it is
detected and either avoided or corrected.

[more info][13571]

Metalloprotein Database and Browser
[Scripps Reasearch Institute] TSRI’s Metalloprotein site Database and Browser (MDB), is a database that aims to contain quantitative
information on all the metal containing sites available from structures in the PDB distribution, as well as from
in-house (TSRI) structures.

[more info][13791]