INTREPED 2.0 – DNA Repair Protein Prediction server

INTREPED 2.0

:: DESCRIPTION

The INTREPED (INTeractive dna REPair prEDiction) web server is a collection of services for predicting properties relating to DNA repair. DNA repair is thought to exist in all organisms that have an active metabolism, and repair systems are crucial for repairing many types of DNA damage. External damage includes (but is not limited to) ionizing (UV) radiation, tobacco smoke, and chemical alteration. Examples of internal damage are DNA copying errors, oxygen byproducts resulting from metabolism, and hydrolysis.

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Jan 20;10:25. doi: 10.1186/1471-2105-10-25.
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.
Brown JB, Akutsu T.

GEDS – Gene Expression Display Server

GEDS

:: DESCRIPTION

GEDS is an integrative platform to show human gene expressions in cancer types, normal tissues and cell lines for user input genes, miRNAs and proteins.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Xia M, Liu CJ, Zhang Q, Guo AY.
GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins.
Cells. 2019 Jul 3;8(7):675. doi: 10.3390/cells8070675. PMID: 31277321; PMCID: PMC6678772.

MISTIC – Mutual Information Server to Infer Coevolution

MISTIC

:: DESCRIPTION

MISTIC is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families.

::DEVELOPER

Structural Bioinformatics Unit, Fundación Instituto Leloir

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W8-14. doi: 10.1093/nar/gkt427. Epub 2013 May 28.
MISTIC: Mutual information server to infer coevolution.
Simonetti FL1, Teppa E, Chernomoretz A, Nielsen M, Marino Buslje C.

LactFP – β-Lactamase Fingerprint Prediction Server

LactFP

:: DESCRIPTION

LactFP find signature in query protein sequence belong to specific b-lactamase family.In response to query protein submission, it finds the family specific pattern.

::DEVELOPER

LactFP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

WEb browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

ScientificWorldJournal. 2014 Feb 11;2014:980572. doi: 10.1155/2014/980572. eCollection 2014.
Identification of family specific fingerprints in β-lactamase families.
Srivastava A1, Singhal N2, Goel M1, Virdi JS2, Kumar M

CCTOP 1.00 – Constrained Consensus TOPology prediction server

CCTOP 1.00

:: DESCRIPTION

CCTOP server is a web-based application providing transmembrane topology prediction.

::DEVELOPER

CCTOP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CCTOP

:: MORE INFORMATION

Citation

CCTOP: a Consensus Constrained TOPology prediction web server.
Dobson L, Reményi I, Tusnády GE.
Nucleic Acids Res. 2015 May 5. pii: gkv451

RBO Aleph – Protein Contact and Structure Prediction Server

RBO Aleph

:: DESCRIPTION

RBO Aleph is a novel server for fully automated protein structure prediction. The server implements template-based modeling, protein contact prediction, and ab initio structure prediction.

::DEVELOPER

the Robotics and Biology Lab (RBO), Technische Universität Berlin.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

RBO Aleph: leveraging novel information sources for protein structure prediction.
Mabrouk M, Putz I, Werner T, Schneider M, Neeb M, Bartels P, Brock O.
Nucleic Acids Res. 2015 Apr 20. pii: gkv357.

MapMyFlu 2.0 – Blast-server for Influenza Sequences

MapMyFlu 2.0

:: DESCRIPTION

MapMyFlu is a blast-server for influenza sequences (protein or DNA) which displays the top hits using Google Maps in a spatial and temporal fashion.

::DEVELOPER

MapMyFlu team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences.
Nolte N, Kurzawa N, Eils R, Herrmann C.
Nucleic Acids Res. 2015 May 4. pii: gkv417.

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

:: 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

PROFEAT 2016 – Protein Feature Server

PROFEAT 2016

:: DESCRIPTION

PROFEAT is developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence and of small molecules from molecular structure.

::DEVELOPER

Bioinformatics & Drug Design group [BIDD]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W385-90. doi: 10.1093/nar/gkr284. Epub 2011 May 23.
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence.
Rao HB1, Zhu F, Yang GB, Li ZR, Chen YZ.

PISCES 20210711 – Protein Sequence Culling Server

PISCES 20210711

:: DESCRIPTION

PISCES (Protein Sequence Culling Server) is a database server for producing lists of sequences from the Protein Data Bank (PDB) using a number of entry- and chain-specific criteria and mutual sequence identity.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux
Perl

:: DOWNLOAD

PISCES

:: MORE INFORMATION

Citation

Guoli Wang and Roland L. Dunbrack Jr.
“PISCES: a protein sequence culling server“,
Bioinformatics 19:1589-1591, 2003.