Bioinformatics & Genomics
3-D Structure Prediction
Protein Data Bank (PDB)
Searches of PDB
Secondary Structure Prediction & Assignment
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[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.
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.
[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.
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.
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.
[UCLA] A protein structure verification algorithm that analyzes the statistics of non-bonded interactions between different atom types.
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.
[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.
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.
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.
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Online Macromolecular Museum
[California Lutheran College] The OMM is a site for the display and study of macromolecules. It’s “exhibits” are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand.
Protein Modeling Software and Services
[University of California, San Francisco] Access to protein modeling programs produced in the Fred Cohen Laboratory.
Protein Topology Home Page
[EBI] This site offers services devoted to protein structural topology and protein topology cartoons.
Secondary Structure Alignment Server
[Rutgers] The secondary structure alignment server is an
interactive tool that allows sequence alignments
to be performed based on iterative combinations
of amino acid and secondary structure sequence
[Drug Design Laboratory, Milan University] VEGA was developed to create a bridge between most of the molecular software
packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, etc. Also implemented are some features that are useful to analyze, display
and manage the 3D structures of molecules. Features include: atomic charge attribution, force field attribution, calculation of molecular surfaces, calculation of ligand-receptor interaction energy, evaluation of logP and lipole, dynamic trajectory analysis, and molecule solvatation.
[UCLA-DOE] A tool designed to help in the refinement of crystallographic structures, it provides a visual analysis of the quality of a putative crystal structure for a protein.