i3Drefine / 3Drefine – Protein 3D Structure Refinement

i3Drefine / 3Drefine

:: DESCRIPTION

i3Drefine is a completely automated and computationally efficient protein 3D structure refinement method which based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique.

3Drefine: protein structure refinement server

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 i3Drefine

:: MORE INFORMATION

Citation

3Drefine: an interactive web server for efficient protein structure refinement.
Bhattacharya D, Nowotny J, Cao R, Cheng J.
Nucleic Acids Res. 2016 Apr 29. pii: gkw336

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
Bhattacharya D, Cheng J.
Proteins. 2013 Jan;81(1):119-31. doi: 10.1002/prot.24167.

PLoS One. 2013 Jul 19;8(7):e69648. doi: 10.1371/journal.pone.0069648. Print 2013.
i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
Bhattacharya D1, Cheng J.

MCMC5C – Prediction of Chromatin 3D Structure

MCMC5C

:: DESCRIPTION

MCMC5C is a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach to generate a representative sample from the posterior distribution over structures from IF data.

::DEVELOPER

Dr. Josée Dostie Lab

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 MCMC5C

:: MORE INFORMATION

Citation

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.
Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M.
BMC Bioinformatics. 2011 Oct 25;12:414. doi: 10.1186/1471-2105-12-414.

R3D Align – RNA 3D Structure Alignment

R3D Align

:: DESCRIPTION

R3D Align is a web application for locally optimized, nucleotide to nucleotide pairwise alignments of RNA 3D structure

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

R3D Align

:: MORE INFORMATION

Citation

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W15-21. doi: 10.1093/nar/gkt417.

FR3D 20120611 / WebFR3D – Find Structural Motifs in RNA 3D Structures

FR3D 20120611 / WebFR3D

:: DESCRIPTION

FR3D stands for “Find RNA 3D” and is commonly pronounced “Fred”.  It was developed to find small RNA motifs (two to 20 nucleotides) in PDB files.

WebFR3D is the online version of FR3D, a suite of Matlab programs designed to search RNA 3D structures for user specified queries.

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

 FR3D

:: MORE INFORMATION

Citation:

Michael Sarver; Craig L. Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B. Leontis.
FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures,
Journal of Mathematical Biology (2008) 56:215–252.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W50-5. doi: 10.1093/nar/gkr249. Epub 2011 Apr 22.
WebFR3D–a server for finding, aligning and analyzing recurrent RNA 3D motifs.
Petrov AI1, Zirbel CL, Leontis NB.

iDBPs – Identification of DNA Binding Proteins (DBPs) for Proteins with known 3D-structure

iDBPs

:: DESCRIPTION

The iDBPs server was developed for the identification of DNA binding proteins (DBPs) for proteins with known three-dimensional structure

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Mar 1;26(5):692-3. doi: 10.1093/bioinformatics/btq019. Epub 2010 Jan 19.
iDBPs: a web server for the identification of DNA binding proteins.
Nimrod G, Schushan M, Szilágyi A, Leslie C, Ben-Tal N.

ConTemplate – Server for Suggesting Alternative Conformations for a query Protein with one known 3D structure

ConTemplate

:: DESCRIPTION

ConTemplate is an automatic computational tool for suggesting alternative conformations for a query protein with one known structure based on the conformational repertoire in the Protein Data Bank (PDB).

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Structure. 2015 Nov 3;23(11):2162-70. doi: 10.1016/j.str.2015.08.018. Epub 2015 Oct 9.
ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure.
Narunsky A, Nepomnyachiy S, Ashkenazy H, Kolodny R, Ben-Tal N.

PONDEROSA-C/S 20151030 – Automated Protein 3D structure Determination

PONDEROSA-C/S 20151030

:: DESCRIPTION

PONDEROSA-C/S  is a successor of the PONDEROSA (Peak picking Of NOE Data Enabled by Restriction Of Shift Assignments) program, which utilizes information from prior assignments to automatically pick NOE peaks from 3D-NOESY (13C-edited and 15N-edited) spectra and uses the results as input for a series of AUDANA (Automated Database-Assisted NOE Assignment) or CYANA structure calculations with the goal of achieving a publishable quality solution structure.

::DEVELOPER

The National Magnetic Resonance Facility at Madison (NMRFAM)

:: SCREENSHOTS

Ponderosa

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

PONDEROSA-C/S

:: MORE INFORMATION

Citation

Lee W, Stark JL, Markley JL. (2014)
PONDEROSA-C/S: Client-server based software package for automated protein 3D structure determination.
Journal of Biomolecular NMR 60(2-3):73-5

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.
Lee W, Kim JH, Westler WM, Markley JL.
Bioinformatics. 2011 Jun 15;27(12):1727-8. doi: 10.1093/bioinformatics/btr200.

GDFuzz3D – Protein 2D Map to 3D Structure Retrieval Service

GDFuzz3D

:: DESCRIPTION

GDFuzz3D is a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.

::DEVELOPER

Bujnicki Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GDFuzz3D

:: MORE INFORMATION

Citation

GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.
Pietal MJ, Bujnicki JM, Kozlowski LP.
Bioinformatics. 2015 Jun 30. pii: btv390.

RNAssess – Quality Assessment of RNA 3D Structures

RNAssess

:: DESCRIPTION

RNAssess is a computational server for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models.

::DEVELOPER

RNAssess team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNAssess-a web server for quality assessment of RNA 3D structures.
Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J.
Nucleic Acids Res. 2015 Jun 11. pii: gkv557.

R3D-2-MSA – RNA 3D Structure-to-Multiple Sequence Alignment Server

R3D-2-MSA

:: DESCRIPTION

R3D-2-MSA enables users to select nucleotides from representative RNA 3D structures and seamlessly access sequence variants from large and diverse sequence alignments.

::DEVELOPER

Leontis-Zirbel Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Jun 5. pii: gkv543.
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N