Links tagged with 'macromolecular substances'

Found 17 links

Displaying 15 links

EMDataBank.orgDatabase Content

Share This Link 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 unified data resource for CryoEM201115

H++Tool Content

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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

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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

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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

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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

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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

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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

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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.

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