Discriminative HMMs – Find Discriminative Motif to Predict Protein Subcellular Localization

Discriminative HMMs

:: DESCRIPTION

Discriminative HMMs (Hidden Markov models) predicts localizations using motifs that are present in a compartment but absent in other, nearby, compartments by utilizing an hierarchical structure that mimics the protein sorting mechanism.

::DEVELOPER

Tien-ho LinRobert F. Murphy, and Ziv Bar-Joseph

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Discriminative HMMs

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):441-51.
Discriminative motif finding for predicting protein subcellular localization.
Lin TH, Murphy RF, Bar-Joseph Z.

StarORF – Identification of the Protein(s) Encoded within a DNA sequence

StarORF

:: DESCRIPTION

StarORF facilitates the identification of the protein(s) encoded within a DNA sequence. Using StarORF, the DNA sequence is first transcribed into RNA and then translated into all the potential ORFs (Open Reading Frame) encoded within each of the six translation frames (3 in the forward direction and 3 in the reverse direction).

:: DEVELOPER

The STAR program at MIT

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 StarORF

:: MORE INFORMATION

AcconPred 1.00 – Predicting Solvent Accessibility and Contact Number of Protein

AcconPred 1.00

:: DESCRIPTION

AcconPred is a software package that helps predicting solvent accessibility and contact number of a protein simultaneously.

::DEVELOPER

Sheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AcconPred

:: MORE INFORMATION

Citation:

Ma J, Wang S.
AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model.
Biomed Res Int. 2015;2015:678764. doi: 10.1155/2015/678764. Epub 2015 Aug 3. PMID: 26339631; PMCID: PMC4538422.

ProtASR 2.2 – Ancestral Sequence Reconstruction of Proteins accounting for Structural Constraints

ProtASR 2.2

:: DESCRIPTION

ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.

::DEVELOPER

CME Group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProtASR

:: MORE INFORMATION

Citation

Arenas M, Weber CC, Liberles DA, Bastolla U.
ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.
Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121. PMID: 28057858.

CMView 1.1.1 – Protein Contact Map Visualization and Analysis

CMView 1.1.1

:: DESCRIPTION

CMView is an intervative contact map visualization and analysis tool. The tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.

::DEVELOPER

CMView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 CMView

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1573-4. Epub 2011 Apr 5.
CMView: interactive contact map visualization and analysis.
Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M.

Hollow 1.3 – Illustration software for Proteins

Hollow 1.3

:: DESCRIPTION

HOLLOW facilitates the production of surface images of proteins. Hollow generates fake atoms that identifies voids, pockets, channels and depressions in a protein structure specified in the PDB format.

::DEVELOPER

Hollow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Python

:: DOWNLOAD

Hollow

:: MORE INFORMATION

Bosco K. Ho and Franz Gruswitz
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures (2008)
BMC Structural Biology 8:49

ProtDeform 1.0 – Protein Structural Alignment

ProtDeform 1.0

:: DESCRIPTION

ProtDeform is a protein structural alignment. It automatically finds the alignments that expert hands define as most likely, and to recognize domains with the same CATH homology and topology.

::DEVELOPER

Computational Biology and Bioinformatics Research Group , University of the Balearic Islands

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 ProtDeform

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jul 1;25(13):1625-31. doi: 10.1093/bioinformatics/btp296.
Flexible structural protein alignment by a sequence of local transformations.
Rocha J, Segura J, Wilson RC, Dasgupta S.

PESS 1.0.0 – Full-scale Protein Fold Recognition using 1NN

PESS 1.0.0

:: DESCRIPTION

PESS (Protein Empirical Structure Space) is a software of sensitive protein fold recognition using an empirical structure space and 1NN.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PESS

:: MORE INFORMATION

Citation

Middleton SA, Illuminati J, Kim J.
Complete fold annotation of the human proteome using a novel structural feature space.
Sci Rep. 2017 Apr 13;7:46321. doi: 10.1038/srep46321. PMID: 28406174; PMCID: PMC5390313.

LACS – Validate Protein NMR Chemical Shifts

LACS

:: DESCRIPTION

LACS ( linear analysis of chemical shifts) is a validation tool for protein backbone NMR chemical shift data. Based on the observation that secondary chemical shift (difference between the chemical shift of an amino acid and its random coil chemical shift) well indicate the local backbone geometry, LACS correlates the secondary chemical shifts of a nucleus to that of Ca-Cb of itself (referencing independent), thus avoiding any geometry or structure assumptions, to estimate referencing offsets and identify possible miss-assignments.

::DEVELOPER

Liya Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 LACS

:: MORE INFORMATION

Citation

Wang, L.; Eghbalnia, H. R.; Bahrami, A.; Markley, J. L.,
Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications,
J. Biomol. NMR 25, 32, 13-22.

Surface Diver – Comparing, and Classifying Proteins according to their Physicochemical Properties

Surface Diver

:: DESCRIPTION

Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Surface Diver

:: MORE INFORMATION

Citation

Maciej Dlugosz, Joanna Trylska
Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition,
J. Chem. Phys., 129:015103, 2008

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