HiCNet – Reconstruct High-resolution Chromosome 3D Structures based on Hi-C Complex Networks

HiCNet

:: DESCRIPTION

HiCNet is an approach for establishing small-world networks for individual chromosomes using Hi-C data. It is a tool capable of converting Hi-C contacts to spatial distances. And it can also infer three-dimensional structures using spatial distances and multidimensional scaling methods.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

HiCNet

:: MORE INFORMATION

Citation

Liu T, Wang Z.
Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks.
BMC Bioinformatics. 2018 Dec 28;19(Suppl 17):496. doi: 10.1186/s12859-018-2464-z. PMID: 30591009; PMCID: PMC6309071.

KYG – RNA Interface Residue Prediction from Protein 3D Structure

KYG

:: DESCRIPTION

KYG predicts RNA interfaces out of 3D structures of RNA-binding proteins.

::DEVELOPER

Center for Informational Biology, Ochanomizu University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ COmpiler

:: DOWNLOAD

KYG

:: MORE INFORMATION

Citation

Kim, O.T.P., Yura, K., Go, N. (2006)
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction.
Nuc. Acids. Res. 34 (22), 6450-6460.

MotAn ver. beta.1603061903 – Motif Analyzer for Protein 3D Structures

MotAn ver. beta.1603061903

:: DESCRIPTION

MotAn detects structural motifs containing β-strands

::DEVELOPER

Evgeniy Aksianov (evaksianov@gmail.com)

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/Linux

:: DOWNLOAD

MotAn

:: MORE INFORMATION

Citation

J Struct Biol. 2014 Mar 4. pii: S1047-8477(14)00051-3. doi: 10.1016/j.jsb.2014.02.017.
Motif Analyzer for protein 3D structures.
Aksianov E.

GIANT – Pattern analysis of Molecular Interactions in 3D Structures of Protein–small Ligand Complexes

GIANT

:: DESCRIPTION

GIANT (Gaussian mixture model-based Interaction ANalyzer focusing on Three-atom fragments)is a web server for pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.

::DEVELOPER

GIANT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web server

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jan 14;15:12. doi: 10.1186/1471-2105-15-12.
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.
Kasahara K, Kinoshita K

PONDEROSA-C/S 20181026 – Automated Protein 3D structure Determination

PONDEROSA-C/S 20181026

:: 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

:: 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.

AutoChrom3D v1 – Modeling and Visualization the 3D Structure of Human or Mouse Chromatin

AutoChrom3D v1

:: DESCRIPTION

AutoChrom3D was built for modeling and visualization the 3D structure of human or mouse chromatin. The 3D structure of chromatin is calculated and generated based on HiC data.

::DEVELOPER

PENG Cheng (email: pengcheng@mail.hzau.edu.cn).

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

AutoChrom3D

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Oct;41(19):e183. doi: 10.1093/nar/gkt745. Epub 2013 Aug 21.
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C1, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, Zhang HY.

tREX – Reconstruction of 3D structure of Chromatins using Hi-C data

tREX

:: DESCRIPTION

tPAM and tREX(truncated Random effect EXpression) are codes for reconstruction of 3D structure of chromatins using Hi-C data based on two model-based algorithms.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

tREX

:: MORE INFORMATION

Citation

BMC Bioinformatics, 17, 70 2016 Feb 6
Impact of Data Resolution on Three-Dimensional Structure Inference Methods
Jincheol Park, Shili Lin

RASMOT-3D PRO – Recursive Automatic Search of MOTif in 3D structures of PROteins

RASMOT-3D PRO

:: DESCRIPTION

RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by a 3D motif given in input.

::DEVELOPER

CEA, LIFE SCIENCES DIVISION

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W459-64. doi: 10.1093/nar/gkp304. Epub 2009 May 5.
RASMOT-3D PRO: a 3D motif search webserver.
Debret G1, Martel A, Cuniasse P.

STON – Protein 3D Structure Comparison

STON

:: DESCRIPTION

STON is a new algorithm to find aligned residues in two proteins with desired rmsd value.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Comput Biol Med. 2009 Feb;39(2):166-72. doi: 10.1016/j.compbiomed.2008.12.004. Epub 2009 Jan 23.
STON: A novel method for protein three-dimensional structure comparison.
Eslahchi C1, Pezeshk H, Sadeghi M, Massoud Rahimi A, Maboudi Afkham H, Arab S.

CompAnnotate 1.5 – Annotate base-pairing Interactions in RNA 3D Structures.

CompAnnotate 1.5

:: DESCRIPTION

CompAnnotate is a program for annotation of RNA using comparative method. A better annotation is generated for a low resolution ‘target PDB’ with the help of a high resolution ‘reference PDB’.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CompAnnotate

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2017 Aug 21;45(14):e136. doi: 10.1093/nar/gkx538.
CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.
Islam S, Ge P, Zhang S.