FlexPred – Protein Fluctuation Prediction using SVR

FlexPred

:: DESCRIPTION

FlexPred predicts real-value fluctuation of each residues in a query protein structure. Predication can be performed for single-chain, complex proteins, and computational models.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Methods Mol Biol. 2017;1484:175-186. doi: 10.1007/978-1-4939-6406-2_13.
Predicting Real-Valued Protein Residue Fluctuation Using FlexPred.
Peterson L, Jamroz M, Kolinski A, Kihara D

Emap2sec – Protein secondary structure detection in intermediate-resolution cryo-EM maps

Emap2sec

:: DESCRIPTION

Emap2sec is a deep learning-based tool for detecting protein secondary structures from intermediate resolution cryo-EM maps.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Emap2sec

:: MORE INFORMATION

Citation

Nat Methods. 2019 Sep;16(9):911-917. doi: 10.1038/s41592-019-0500-1. Epub 2019 Jul 29.
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.
Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D.

Patch-Surfer 2.0 / PL-PatchSurfer2 – Prediction of Binding Ligand for a Protein

Patch-Surfer 2.0 / PL-PatchSurfer2

:: DESCRIPTION

Patch-Surfer is a method used to predict the binding ligand for a protein. The method used the 3 Dimensional Zernike Descriptor (3DZD) and Approximate Patch Position (APP) to describe the features of different patches of the protein pocket. Then retrieve similar pockets in the pocket database based on the similarity of 3DZD and APP between patches of different pockets, so that to predict the binding ligand.

PL-PatchSurfer2 is a protein ligand virtual screening program that uses local surface matching between ligand and receptor pocket.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser / Linux

:: DOWNLOAD

PL-PatchSurfer2

:: MORE INFORMATION

Citation

PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.
Hu B, Zhu X, Monroe L, Bures MG, Kihara D.
Int J Mol Sci. 2014 Aug 27;15(9):15122-45. doi: 10.3390/ijms150915122.

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.
Zhu X, Xiong Y, Kihara D.
Bioinformatics. 2014 Oct 29. pii: btu724.

cleverSuite – Protein Characterization

cleverSuite

:: DESCRIPTION

the cleverSuite is an approach for large-scale characterization of protein groups.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1601-8. doi: 10.1093/bioinformatics/btu074. Epub 2014 Feb 3.
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities.
Klus P, Bolognesi B, Agostini F, Marchese D, Zanzoni A, Tartaglia GG.

PAnDA – Protein And DNA Associations

PAnDA

:: DESCRIPTION

PAnDA is an algorithm for the prediction of direct and indirect TF binding events.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Oct 30;43(19):e125. doi: 10.1093/nar/gkv607. Epub 2015 Jun 18.
By the company they keep: interaction networks define the binding ability of transcription factors.
Cirillo D, Botta-Orfila T, Tartaglia GG

SHIFTS 5.5 – Predict Nitrogen, Carbon & Proton Chemical Shifts in Proteins

SHIFTS 5.5

:: DESCRIPTION

SHIFTS takes a protein structure in Brookhaven (PDB) format, and computes proton chemical shifts from empirical formulas. It can also compute N, C`alpha`, C`beta` and C’ shifts in proteins, using a database based on DFT calculations on peptides.

Shifts Web Version

::DEVELOPER

the Case group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

SHIFTS

:: MORE INFORMATION

Citation

X.P. Xu and D.A. Case.
Probing multiple effects on 15N, 13Ca, 13Cb and 13C’ chemical shifts in peptides using density functional theory.
Biopolymers 65 408-423 (2002).

jEcho 1.0C – An Evolved Weight Vector to CHaracterize the protein’s post-translational Modification mOtifs

jEcho 1.0C

:: DESCRIPTION

jEcho is an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

jEcho

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Java

:: DOWNLOAD

 jEcho

:: MORE INFORMATION

Citation

Interdiscip Sci. 2015 Jun;7(2):194-9. doi: 10.1007/s12539-015-0260-2. Epub 2015 Aug 6.
jEcho: an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.
Zhao M, Zhang Z, Mai G, Luo Y, Zhou F.

CaverDock 1.01 – Analysis of Transport Processes in proteins

CaverDock 1.01

:: DESCRIPTION

CaverDock is a new tool for an extremely rapid analysis of transportation processes in proteins. It models the transportation of a ligand (a substrate, a product, an inhibitor, a co-factor or a co-solvent) from the outside environment into the binding site and vice versa.

::DEVELOPER

Protein Engineering Group, Loschmidt Laboratories

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CaverDock

:: MORE INFORMATION

Citation

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.
Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J.
Bioinformatics. 2019 Dec 1;35(23):4986-4993. doi: 10.1093/bioinformatics/btz386.

CalFitter 1.3 – Analysis of Protein Thermal Denaturation data

 

CalFitter 1.3

:: DESCRIPTION

CalFitter is a computational tool for an analysis and fitting of calorimetric protein melting curves obtained from differential scanning calorimetry (DSC) measurements.

::DEVELOPER

Protein Engineering Group, Loschmidt Laboratories

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

CalFitter

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2018 Jul 2;46(W1):W344-W349. doi: 10.1093/nar/gky358.
CalFitter: a web server for analysis of protein thermal denaturation data.
Mazurenko S, Stourac J, Kunka A, Nedeljkovic S, Bednar D, Prokop Z, Damborsky J

INTERSPIA – INTER-Species Protein Interaction Analysis

INTERSPIA

:: DESCRIPTION

INTERSPIA is a web-based application for the analysis and visualization of the dynamics of protein-protein interactions among multiple species.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.
Kwon D, Lee D, Kim J, Lee J, Sim M, Kim J.
Nucleic Acids Res. 2018 Jul 2;46(W1):W89-W94. doi: 10.1093/nar/gky378.