Tag: Amino Acids

Forcefield_NCAA – AMBER Forcefield Parameters for Non-canonical Amino Acids

Forcefield_NCAA / FFNCAA

:: DESCRIPTION

Forcefield_NCAA is a set of self-consistent AMBER forcefield parameters for non-canonical amino acids. It allows you to design and derivatize peptides containing NCAAs for use as drugs.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.
Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA.
ACS Synth Biol. 2014 Dec 19;3(12):855-69. doi: 10.1021/sb400168u.

SAAMBE – Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

SAAMBE

:: DESCRIPTION

SAAMBE (Single Amino Acid Mutation related change of Binding Energy) method addresses the demand for computational tools of predicting the effect of single amino acid substitution on the binding free energy of protein complexes. It is based on the fast (<< 1 minute) modified MM-PBSA protocol that is successfully tested and optimized for more than thousand experimental data points.

::DEVELOPER

Professor Emil Alexov Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.
Petukh M, Dai L, Alexov E.
Int J Mol Sci. 2016 Apr 12;17(4). pii: E547.

BcePred – Predict B cell Epitope based on Physio-chemical Properties of Amino Acids

BcePred

:: DESCRIPTION

The BcePred server predicts B cell epitope based on physio-chemical properties of amino acids.

::DEVELOPER

BcePred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha.S and Raghava G.P.S.
BcePred:Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties.
In G.Nicosia, V.Cutello, P.J. Bentley and J.Timis (Eds.) ICARIS 2004, LNCS 3239, 197-204, Springer,2004.

Alphabet – Find Groups of Amino Acids that Co-occur in Columns Frequently

Alphabet

:: DESCRIPTION

Alphabet takes a database of aligned protein sequences in BLOCKS+ format and examines the alignments column-wise looking for groups of amino acids that co-occur in columns more frequently than expected based on overall amino acid composition. These groups of amino acids can form a reduced alphabet for building sequence motifs (eMOTIFs) or for detecting correlations between columns of amino acids (MCSeq).

:DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 Alphabet

:: MORE INFORMATION

Citation:

Wu, T. D. and Brutlag, D. L. (1996).
Discovering Empirically Conserved Amino Acid Substitution Groups in Databases of Protein Families.
ISMB-96, 3, 230-240.