HDOCK 1.1 – Protein-protein and Protein-DNA/RNA Docking based on Hybrid Strategy

HDOCK 1.1

:: DESCRIPTION

The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

HDOCK

:: MORE INFORMATION

Citation:

Yan Y, Zhang D, Zhou P, Li B, Huang SY.
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W365-W373. doi: 10.1093/nar/gkx407. PMID: 28521030; PMCID: PMC5793843.

Gelapp 1.2.7 – DNA & Prot Gel Analyzer

Gelapp 1.2.7

:: DESCRIPTION

Gelapp is an app that allows you to analyze gel (both agarose and PAGE) bands with a log graph automatically generated from the markers. It allows automatic detection and loading for future uses. Utilizing Gabor filter, this app allows users to improve detection of bands automatically. For poor quality images, users can click can manually draw a box on the desired band or click on the image to determine the specified location.

::DEVELOPER

Antibody & Product Development Team of BII-p53Lab ASTAR

:: SCREENSHOTS

:: REQUIREMENTS

iOS / Android

:: DOWNLOAD

Gelapp for iOS / for Android.

:: MORE INFORMATION

Citation

Nguyen PV, Ghezal A, Hsueh YC, Boudier T, Gan SK, Lee HK.
Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.
Electrophoresis. 2016 Aug;37(15-16):2208-16. doi: 10.1002/elps.201600197. Epub 2016 Jul 4. PMID: 27251892.

DBRandomizer – Randomizes DNA and protein databases

DBRandomizer

:: DESCRIPTION

DBRandomizer randomizes DNA and protein databases in different ways(Markov Chain DB, Shuffle DB, Reverse DB).

:: DEVELOPER

AgBase, Department of Basic Science,College of Veterinary Medicine, Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows /Linux/MacOsX
Perl

:: DOWNLOAD

DBRandomizer

:: MORE INFORMATION

iRO-3wPseKNC / iRO-PsekGCC- Identify DNA Replication Origins

iRO-3wPseKNC / iRO-PsekGCC

:: DESCRIPTION

iRO-3wPseKNC is a webserver of identify DNA replication origins by three-window-based PseKNC

iRO-PsekGCC is a web server to identify DNA replication origins based on Pseudo k-tuple GC Composition

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Liu B, Weng F, Huang DS, Chou KC.
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC.
Bioinformatics. 2018 Sep 15;34(18):3086-3093. doi: 10.1093/bioinformatics/bty312. PMID: 29684124.

Liu B, Chen S, Yan K, Weng F.
iRO-PsekGCC: Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition.
Front Genet. 2019 Sep 18;10:842. doi: 10.3389/fgene.2019.00842. PMID: 31620165; PMCID: PMC6759546.

BioSeq-Analysis 2.0 / BioSeq-BLM 1.0 – Analyzing DNA, RNA, and Protein Sequences based on Biological Language Models

BioSeq-Analysis 2.0 / BioSeq-BLM 1.0

:: DESCRIPTION

BioSeq-Analysis is an platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches

BioSeq-BLM is a platform for analyzing DNA, RNA, and protein sequences based on biological language models

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

BioSeq-Analysis / BioSeq-BLM

:: MORE INFORMATION

Citation

Liu B, Gao X, Zhang H.
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches.
Nucleic Acids Res. 2019 Nov 18;47(20):e127. doi: 10.1093/nar/gkz740. PMID: 31504851; PMCID: PMC6847461.

Pse-in-One 1.0.6 – Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences

Pse-in-One 1.0.6

:: DESCRIPTION

Pse-in-One is a web server for generating various modes of pseudo components of DNA, RNA and protein sequences

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

Pse-in-One

:: MORE INFORMATION

Citation

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Liu B, Liu F, Wang X, Chen J, Fang L, Chou KC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71. doi: 10.1093/nar/gkv458.

POY 5.1.1 – Phylogenetic Analysis of DNA and other data using Dynamic Homology

POY 5.1.1

:: DESCRIPTION

POY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned). Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likelihood). A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.

::DEVELOPER

Systematic Biology divisions of the AMNH

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX/ Windows / Linux

:: DOWNLOAD

POY

:: MORE INFORMATION

Citation

Varón, A., L. S. Vinh, W. C. Wheeler. 2010.
POY version 4: phylogenetic analysis using dynamic homologies.
Cladistics, 26:72-85.

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

:: 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.

srnaloop – Search long DNA/RNA Strings for small RNA Hairpin Loops

srnaloop

:: DESCRIPTION

srnaloop searchs long DNA/RNA strings for small RNA hairpin loops that may be candidates for small RNA regulatory sequences.

::DEVELOPER

George M. Church Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
C Compiler

:: DOWNLOAD

srnaloop

:: MORE INFORMATION

Citation

Mol Cell. 2003 May;11(5):1253-63.
Computational and experimental identification of C. elegans microRNAs.
Grad Y1, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J.

DNAFSMiner – DNA Functional Site Miner

DNAFSMiner

:: DESCRIPTION

DNAFSMiner is a web-based software toolbox that aims to predict these functional sites in DNA sequences.Currently, there are two software tools. One is called TIS Miner which can be used to predict translation initiation site (TIS) in vertebrate mRNA, cDNA, or DNA sequences. The other is called Poly(A) Signal Miner which can be used to predict polyadenylation (poly(A)) signal in human DNA sequences.

::DEVELOPER

DNAFSMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Mar 1;21(5):671-3. Epub 2004 Jul 29.
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences.
Liu H1, Han H, Li J, Wong L.