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- BioStar@biostar
BioStar bookmarked VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening 1624 days ago

related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM). Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks: VFLP:...

https://virtual-flow.org/
- BioStar@biostar
BioStar bookmarked AutoDock Vina: an open-source program for doing molecular docking. 1624 days ago

AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. It is especially effective for protein-ligand...

http://vina.scripps.edu/
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- BioStar@biostar
  
  BioStar 1624 days ago
  QVina-W, a new docking tool particularly useful for wide search space, especially for blind docking. QVina-W utilizes the powerful scoring function of AutoDock Vina, the accelerated search of QVina 2, and adds thorough search for wide search space.
  https://qvina.github.io/
- BioStar@biostar
  
  BioStar 1624 days ago
  AutoDockFR (or ADFR in short) is a protein-ligand docking program developed in the Sanner laboratory at Scripps Research under the AutoDock umbrella.
  https://ccsb.scripps.edu/adfr/
- Jit@jit.aber
Jit bookmarked HS3D: Homo Sapiens Splice Sites Dataset 1625 days ago

HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of...

http://www.sci.unisannio.it/docenti/rampone/
- Neel@neelam
Neel posted to the wire 1625 days ago

Beginner’s guide to #comparative #bacterial #genome analysis using next-generation sequence data https://microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-3-2
- Jit@jit.aber
Jit bookmarked PPAI: a web server for predicting protein-aptamer interactions 1625 days ago

PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is...

http://39.96.85.9/PPAI/
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

Gene and protein expression data of human genes implicated in the virus infection of the host cells. Identifying cell types and genes with highest expression in SARS-CoV-2 infections. https://www.covid19dataportal.org/expression?db=expression
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

Range of SARS-CoV-2 and SARS-CoV data for drug target identification and prioritisation. https://www.covid19dataportal.org/targets?db=complex-portal
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

Curated range of SARS-CoV-2 compound activity data.https://www.covid19dataportal.org/compounds?db=chembl-document
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

Curated functional and classification data on the SARS-CoV-2 protein entries and associated protein receptors. https://www.covid19dataportal.org/proteins?db=uniprot-covid19
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

SARS-CoV-2 protein structures, highlighting important structural features to support the development of treatments and vaccines. https://www.covid19dataportal.org/structures?db=structures
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

Raw and assembled sequences related to the COVID-19 outbreak, including outbreak isolates and records relating to coronavirus biology. Includes extensive sampling information. https://www.covid19dataportal.org/sequences?db=embl
- Jit@jit.aber
Jit commented on a bookmark Coronavirus Resources ! 1625 days ago

Corona virus data resources https://www.covid19dataportal.org/
- Neel@neelam
Neel commented on the blog Tools to detect synteny blocks regions among multiple genomes 1627 days ago

Synteny based tool to arrange contigs "r2cat: synteny plots and comparative assembly" http://bibiserv.techfak.uni-bielefeld.de/r2cat https://academic.oup.com/bioinformatics/article/26/4/570/243369
- Jit@jit.aber
Jit bookmarked StringTie Transcript assembly and quantification for RNA-Seq 1628 days ago

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...

https://ccb.jhu.edu/software/stringtie/
- Shruti Paniwala@shruti
Shruti Paniwala posted to the wire 1628 days ago

Long-read human genome sequencing and its applications https://www.nature.com/articles/s41576-020-0236-x #LongReads #Sequencing #Genome #Review
- Jit@jit.aber
Jit bookmarked Merqury: reference-free quality and phasing assessment for genome assemblies 1631 days ago

Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...

https://github.com/marbl/merqury
- Jit@jit.aber
Jit commented on the blog Tools to detect synteny blocks regions among multiple genomes 1632 days ago

halSynteny is the latest input in computational synteny halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome...
- Poonam Mahapatra@poonam
Poonam Mahapatra bookmarked HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures 1632 days ago

The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...

http://huanglab.phys.hust.edu.cn/hnadock/
- Neel@neelam
Neel posted to the wire 1633 days ago

Application of Support Vector Machines in Bioinformatics https://www.csie.ntu.edu.tw/~p88012/Bio_SVM.pdf #Bioinformatics #Application #SVM
- Jit@jit.aber
Jit bookmarked ShinyGO v0.61: Gene Ontology Enrichment Analysis + more 1634 days ago

2/3/2020: Now published by Bioinformatics. 11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more. 5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal...

http://bioinformatics.sdstate.edu/go/

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