:: DESCRIPTION
Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.
::DEVELOPER
Biomolecular Machines Laboratory
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Maciej Dlugosz, Joanna Trylska
Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition,
J. Chem. Phys., 129:015103, 2008
:: DESCRIPTION
CSM-lig is a web server tailored to predict the binding affinity of a protein-small molecule complex based on structural signatures.
mCSM-lig is a structure-guided in silico approach for directly quantifying the effects of single-point missense mutations on affinities of small molecules for proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pires DE, Blundell TL, Ascher DB.
mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance.
Sci Rep. 2016 Jul 7;6:29575. doi: 10.1038/srep29575. PMID: 27384129; PMCID: PMC4935856.
CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Pires DE, Ascher DB.
Nucleic Acids Res. 2016 May 5. pii: gkw390.
:: DESCRIPTION
Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 1;30(7):1036-8. doi: 10.1093/bioinformatics/btt747. Epub 2013 Dec 25.
Assimilating genome-scale metabolic reconstructions with modelBorgifier.
Sauls JT1, Buescher JM.
:: DESCRIPTION
gffcompare is a program for comparing, annotating, merging and tracking transcripts in GFF(General Feature Format) files
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pertea G, Pertea M.
GFF Utilities: GffRead and GffCompare.
F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. PMID: 32489650; PMCID: PMC7222033.
:: DESCRIPTION
GeneNomenclatureUtils is a command-line utilities for using MGI, Entrez, HGNC, PubMed, and OMIM files.
::DEVELOPER
Genes to Cognition (G2C)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Phylo-HMRF (Phylogenetic Hidden Markov Random Field model) identifies evolutionary patterns of 3D genome based on multi-species Hi-C data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Cell Syst. 2019 Jun 26;8(6):494-505.e14. doi: 10.1016/j.cels.
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J.
:: DESCRIPTION
TOPD/FMTS (TOPological Distance / From Multiple To Single)is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Puigbo P., Garcia-Vallve S. and McInerney J.O. (2007)
TOPD/FMTS: a new software to compare phylogenetic trees.
Bioinformatics, 23:1556-1558. doi: 10.1093/bioinformatics/btm135.
:: DESCRIPTION
CompPhy is a web platform dedicated to the collaborative handling of phylogenetic trees.
:: DEVELOPER
The Computational Biology Institute (IBC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Evol Biol. 2014 Dec 14;14(1):253.
CompPhy: a web-based collaborative platform for comparing phylogenies.
Fiorini N, Lefort V, Chevenet F, Berry V, Chifolleau AM.
:: DESCRIPTION
Amordad is a database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 27. pii: btu405. [Epub ahead of print]
The Amordad database engine for metagenomics.
Behnam E, Smith AD.
:: DESCRIPTION
ResProx (Resolution-by-proxy or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Berjanskii M, Zhou J, Liang Y, Lin G, Wishart DS.
J Biomol NMR. 2012 Jul;53(3):167-80. doi: 10.1007/s10858-012-9637-2
