Links tagged with 'macromolecular substances'

Found 17 links

Displaying 15 links

EMDataBank.orgDatabase Content

Share This Link

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
EMDataBank.org: unified data resource for CryoEM201115

H++Tool Content

Share This Link

H++ is an automated tool for computing pK values of ionizable groups in macromolecules and adding missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools useful for analysis of electrostatic-related molecular properties.

This content is being maintained by onufriev.

MONSTERTool Content

Share This Link

MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.

This content is being maintained by samseaver.

NOMAD-RefTool Content

Share This Link

Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.

This content is being maintained by Marc Delarue.

PfamDatabase Content

Share This Link

Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.

POPSCOMPTool Content

Share This Link

POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed.

ProPred1Tool Content

Share This Link

The ProPred-I is an on-line service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles, proteasomal and immunoproteasomal models. The main aim of this server is to help users in identifying the promiscuous regions.

This content is being maintained by raghavagps.

ReadOutTool Content

Share This Link

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

Associated Tag Cloud