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.
[Stanford University] This program takes a PDB file (or ID) as input and compare the query structure to 13,073 domains from the PDB.
[EBI] Service for comparing protein structures in 3D. Protein structure coordinates are submitted for comparison against entries in the Protein Data Bank.
[Laboratories of Molecular Biophysics, Rockefeller University] DBAli is a database that includes approximately 35,000 alignments of pairs of protein structures from SCOP and CE. DBAli is
linked to several resources, including Compare3D and ModView for visualizing sequence alignments and structure
superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of
alignments suitable for benchmarking sequence-sequence and sequence-structure alignment methods under a variety of
[Decodon] Analyze protein 2-dimensional gels. Compare protein spots on two gels with image analysis techniques. Download free demo version or purchase full program.
Finding 3-D Similarity in Protein Structures
[San Diego Supercomputing Center] This site provides two methods for comparing 3D protein structures, and structure neighbor databases derived from them. Combinatorial Extension (CE) determines an optimal alignment between aligned fragment pairs (AFPs). AFPs are
determined from local geometry averaged over 8 C alpha positions. Heuristics are used to prevent a combinatorial
explosion. Final alignments are by dynamic programming. Compound Likeness (CL) uses a probabalistic approach to comparing a wide variety of properties.
[Purdue Univ.] (Guoguang Lu) A program to compare and superimpose two structures using selected atom types and residues.
HOMSTRAD: Homologous Structure Alignment Database
[University of Cambridge] Database provides aligned three-dimensional structures of homologous proteins.
The Live Bench Project is a continuous
benchmarking program. Every week new Protein Data Bank (PDB)
proteins are submitted to all participating
fold recognition servers. The results are
collected and evaluated using automated model
[Stanford University] A server that provides a hierarchical protein structure superposition.
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[Laboratories of Molecular Biophysics, Rockefeller University] ModView is a plugin to visualize and analyze multiple biomolecule structures and/or sequence alignments. It is also used as a database interface in several structure-sequence protein resources: ModBase (database of Comparative Protein Structure Models), LigBase (Structural Database of Aligned Ligand Binding Protein Sequences), and DBAli (database of sequence-structure alignments. ModView can be also used to view structures and sequences in Protein Data Bank.
Molecular Docking Web
[Home page of Dr. Garrett M. Morris] Ligand-protein docking, with access to AutoDock program, important for drug design. Many links for ligands, protein structure, drug design, computational chemistry, bioinformatics.
[Weizmann Institute of Science] MutaProt compares PDB files which differ by point mutations. It provides: a full list of file-pairs which differ by one, or two, amino acids; amino acid neighbors, and atomic contacts, of the mutated residue(s) (based on CSU software); 3D visualization of the mutated region(s) using CHIME; information and definitions page.
SARF2: Spatial ARangement of backbone Fragments
[National Cancer Institute] This is a program (server and downloadable) for spatial arrangement of backbone fragments in protein structures. The goal is to detect 3D similarities of the backbone fragments, without topological restrictions. The idea of the method is to find all the compatible (superimposable) secondary structure elements, and then to form the large ensembles of
mutually compatible elements.
[University College London] The Sequential Structure Alignment Program is a method for automatically comparing three dimensional protein structures using double dynamic programming.
[EBI] “STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only
multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments.”
[Purdue Univ.] Protein topological comparison program that can detect similarities between two protein structures.
TOPSCAN – Rapid Protein Structure Comparison
TOPSCAN is a rapid method for comparing protein structures. It is useful as a preliminary screen to give you some
idea whether your protein looks like something else.
[NCBI] The Vector Alignment Search Tool was used to compare all of the structures in the NCBI MMDB structure database to each other and can now be used as a search to find structural neighbors.
Yale Structure Query Server
[Yale Gerstein Lab] PartsList: a web-based system for dynamically ranking
protein folds based on disparate attributes, including
whole-genome expression and interaction information
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