Tag: Residue

HemeNet – Heme Binding Residue Prediction using Sequence, Structure, and Residue Interaction Network

HemeNet

:: DESCRIPTION

HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(10):e25560. doi: 10.1371/journal.pone.0025560. Epub 2011 Oct 3.
Computational prediction of heme-binding residues by exploiting residue interaction network.
Liu R1, Hu J.

DNABind – DNA Binding Residue Prediction

DNABind

:: DESCRIPTION

DNABind is a novel hybrid algorithm for identifying these crucial residues by exploiting the complementarity between machine learning- and template-based methods.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2013 Nov;81(11):1885-99. doi: 10.1002/prot.24330. Epub 2013 Aug 16.
DNABind: a hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches.
Liu R1, Hu J.

HemeBIND / HemeBIND+ – Heme Binding Residue Prediction from Protein Sequence and Structure

HemeBIND / HemeBIND+

:: DESCRIPTION

HemeBIND is an efficient algorithm for predicting heme binding residues by integrating structural and sequence information.

HemeBIND+ predicts heme-binding residues based on the hybrid machine learning (with structural and sequence features) and template-based approaches.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 May 26;12:207. doi: 10.1186/1471-2105-12-207.
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information.
Liu R1, Hu J.

Validate Fasta File 2.2.7887 – Parse Fasta file and return the number of proteins and number of Residues

Validate Fasta File 2.2.7887

:: DESCRIPTION

The Validate Fasta File utility is a Windows command-line application that will parse a Fasta file and return the number of proteins and number of residues in the file. Additionally, it will check the validity of the fasta file looking for common, known problems.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 4.0

:: DOWNLOAD

 Validate Fasta File utility

:: MORE INFORMATION

FreeContact 1.0.21- Protein Contact Prediction from Residue Co-evolution

FreeContact 1.0.21

:: DESCRIPTION

FreeContact is a protein residue contact predictor optimized for speed.

::DEVELOPER

the Rostlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl /Python

:: DOWNLOAD

 FreeContact

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Mar 26;15:85. doi: 10.1186/1471-2105-15-85.
FreeContact: fast and free software for protein contact prediction from residue co-evolution.
Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B

MotiveValidator 1.1.15.8.8e – Validate Ligand and Residue Structure in Biomolecular Complexes

MotiveValidator 1.1.15.8.8e

:: DESCRIPTION

MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).

::DEVELOPER

MotiveValidator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

MotiveValidator

:: MORE INFORMATION

Citation

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426.

PrISE 20110723 – Prediction of protein-protein Interface residues using Structural Elements

PrISE 20110723

:: DESCRIPTION

PrISE predict interface residues using local surface structural similarity. PrISe represents a local surface structure using structural elements.

::DEVELOPER

Artificial Intelligence Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Mar 18;13:41. doi: 10.1186/1471-2105-13-41.
Predicting protein-protein interface residues using local surface structural similarity.
Jordan RA1, El-Manzalawy Y, Dobbs D, Honavar V.

QUASSI – Quantifying Significance of MHC II Residues

QUASSI

:: DESCRIPTION

QUASSI is a project to solve integer linear programming problem proposed in bioinformatics

::DEVELOPER

QUASSI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE

:: DOWNLOAD

 QUASSI

:: MORE INFORMATION

Citation

Quantifying Significance of MHC II Residues.
Ying Fan, Ruoshui Lu, Lusheng Wang, Andreatta M, Shuai Cheng Li.
IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):17-25. doi: 10.1109/TCBB.2013.138.

CAB-align – Residue-residue Contact Area Based Alignment

CAB-align

:: DESCRIPTION

CAB-align (contact area-based alignment) is a flexible protein structure alignment method based on the residue-residue contact area.

::DEVELOPER

Takeda-Shitaka Lab (Laboratory of Biomolecular Design)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CAB-align

:: MORE INFORMATION

Citation

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.
Terashi G, Takeda-Shitaka M.
PLoS One. 2015 Oct 26;10(10):e0141440. doi: 10.1371/journal.pone.0141440.

PAIRPred 1.0 – Partner Aware Interacting Residue PREDictor

PAIRPred 1.0

:: DESCRIPTION

PAIRPred is a partner specific protein-protein interaction site predictor that can make accurate predictions of whether a pair of residues from two different proteins interact or not.

::DEVELOPER

PAIRPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PAIRPred

:: MORE INFORMATION

Citation

PAIRpred: partner-specific prediction of interacting residues from sequence and structure.
Minhas Fu, Geiss BJ, Ben-Hur A.
Proteins. 2014 Jul;82(7):1142-55. doi: 10.1002/prot.24479.