Coronaviruses

Softwares or packages
MOATAI-VIR MOATAI-VIR predicts disease-protein-pathway relationships for 22 clinical manifestations attributed to COVID-19’s severe adverse events. To the best of our knowledge, this is the first systematic approach to further understand the underlying etiology of COVID-19’s severe responses. More generally, MOATAI-VIR provides a clinically actionable methodology to understand the long-term consequences of viral infections. detial
COVIDScholar This website uses natural language processing (NLP) to power search on a set of research papers related to COVID-19. detial
AIDrugApp This app predicts the inhibitory activities (Active/ Inactive) and IC-50 values of new compounds towards SARS-CoV-2 replicase polyprotein (RP), 3CLpro and human angiotensin converting enzymes (ACE). It is also useful for virtual screening of chemical features of molecules towards SARS-COVID-19 clinical trials (CT) bioactivities. It uses supervised machine learning algorithms with Artificial Neural Network (ANN). detial
Vapur Enter a chemical or protein/gene and let Vapur find related bio-molecules in 150,000 COVID-19 publications! detial
CORD-19 Search Query the COVID-19 Open Research Dataset (CORD-19), with natural language questions and answers from Amazon Kendra. CORD-19 Search includes data from CORD-19 which has been processed using Amazon Comprehend Medical. Data is updated regularly. detial
CROssBAR Use-case COVID-19 Knowledge Graphs detial
WashU Virus Genome Browser Explore the many ways to visualize viral sequencing data on our openly available platform. detial
R2DT Visualise RNA secondary structure in standard orientations using RNA 2D Templates (R2DT). detial
Vapur Enter a chemical or protein/gene and let Vapur find related bio-molecules in 150,000 COVID-19 publications! detial
NETCRIT21J A post hoc analysis of the Noso-Cor study, a multicenter prospective, observational study detial
SARS2020 An Integrated Platform for Identification of Novel Coronavirus by Consensus Sequence-function Model detial
PhyML 3.0 New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies detial
COVID-19 Re The Re for a particular day is the average Re over the three most recent days. We show estimated median Re values together with 95% uncertainty intervals. detial
H2V H2V is a knowledgebase of human genes/proteins that respond to the infection of SARS-CoV-2 (SARS2), SARS-CoV (SARS1), and MERS-CoV. detial
ViruSurf ViruSurf is an integrated search server for virus sequences and their variants. detial
DeepTracer DeepTracer is a fully automatic tool for de novo all-atom protein complex structure prediction from cryo-electron microscopy (cryo-EM) density maps using 3D deep learning. detial
VaxiJen Prediction of Protective Antigens and Subunit Vaccines. detial
genome-sampler A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command detial
Coronavirus3D Web-based viewer for 3D visualization and analysis of the SARS-CoV-2 protein structures with respect to the CoV-2 mutational patterns. detial
NOCOS Northwell COVID‑19 Survival (NOCOS) Calculator detial
coronapp COVID-19 genome annotator detial
METATRYP v 2.0 Testing for the Corona-2 (COVID-19) virus has utilized RNA and antibody analytical methodologies to date. However, there has been recent interest in the potential application of mass spectrometry based proteomic methods as a complement to these methods, which could improve throughput and provide additional capacity for testing during the pandemic. This website has been generated to aid in assay design by utilizing the METATRYP software to determine uniqueness of peptides that can be targeted in diagnostic assays. detial
NetPhos 3.1 Server The NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. detial
MAGA A Supervised Method to Detect Motifs From Annotated Groups in Alignments detial
CovidNLP A Web Application for Distilling Systemic Implications of COVID-19 Pandemic with Natural Language Processing detial
OUTBREAK OUTBREAK facilitates surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak detial
Protein-sol Protein-sol is a simple and free, web based suite of theoretical calculations and predictive algorithms for understanding protein solubility and stability. The software currently has 4 tools. detial
rMAPS2 rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation detial
TREND TREND (TRee-based Exploration of Neighborhoods and Domains): a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses detial
MMFF94 The test molecules for this validation suite consist of 698 structures derived from the Cambridge Structural Database maintained by the Cambridge Crystallographic Data Center (which graciously gave permission for their use) plus 63 additional structures for small molecules and ions, for a total of 761. The native CSD structures were modified by assigning single and multiple bonds, affixing formal ionic charges where appropriate, and adding hydrogens to complete the valence. The resultant structures were minimized to a rms gradient of 0.000001 kcal/mol/A on the MMFF94 energy surface, and were then systematically distorted and re-minimized, and then distorted and re-minimized again. The distortion/re-minimizaton steps were taken to reduce the likelihood that any final conformation represents a very shallow local minimum on the MMFF94 surface, as a molecular-mechanics optimizer might conceivably convert such a conformation to a different local minimum and falsely imply a problem with the implementation of MMFF94 being tested. detial
Brewery Brewery is the state-of-the-art predictor of protein structural annotations (contact density, secondary structure in 3 and 8 classes, solvent accessibility and structural motifs). Brewery is based on ensembles of cascaded BRNNs (bidirectional recurrent neural networks) and Convolutional Neural Networks. detial
YASARA YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux, MacOS and Android developed since 1993, that finally makes it really easy to answer your questions. With an intuitive user interface, photorealistic graphics and support for affordable virtual reality headsets, shutter glasses, autostereoscopic displays and input devices, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. detial
TreeFam TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes. detial
MolProbity More and better reference data for improved all-atom structure validation. detial
T-Coffee T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle, etc.) into one unique alignment (M-coffee).
T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).
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SWISS-MODEL SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make protein modelling accessible to all life science researchers worldwide. detial
libdockapp Simple library that eases the creation of Window Maker dock apps. It provides functions that set up a dock app in such a way that they can be properly docked. It also provides some event handlers and makes it very simple to write dockapps. detial
D3Similarity D3Similarity was developed with two purposes based on the two-dimensional and three-dimensional similarity of molecular structure, one is for predicting target proteins for active compounds observed from experimental studies, and another is for virtual screening via 2D and 3D similarity evaluation. To this end, we developed a database composed of the bioactive molecules with known targets or/and well-explored mechanism related to the whole process of coronavirus infection, replication and release. “TargetPrediction” is for predicting target proteins, while “VirtualScreening” is for virtual screening against target proteins based on the 2D or 3D similarity evaluation. detial
Molegro Virtual Docker Molegro Virtual Docker is an integrated platform for predicting protein – ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.

Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity.

The Molegro Virtual Docker (MVD) has been shown to yield higher docking accuracy than other state-of-the-art docking products (MVD: 87%, Glide: 82%, Surflex: 75%, FlexX: 58%).
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PSORTm - a PSORT tool for metagenomic data PSORTm is a modified version of PSORTb 3.0.2 for protein subcellular localization prediction (SCL), and PSORTdb-based cell envelope classification, that can predict protein SCL from metagenomic sequences. For more information, see the documentation.
Note that unlike PSORTb, PSORTm does not have a web server due to the large size of metagenomic datasets. However, it is available for download in 2 different Docker containers (what is docker?). Which of these you choose to install will depend on how you want to input your metagenomic sequences:
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AutoDock Vina 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. detial
SnapGene Viewer SnapGene Viewer is revolutionary software that allows molecular biologists to create, browse, and share richly annotated DNA sequence files up to 1 Gbp in length. detial
MAFFT MAFFT is a multiple sequence alignment program for unix-like operating systems.? It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences),etc. detial
Virdetect The VirDetect database comprised of 1893 manually-curated vertebrate virus reference genomes from GenBank.To assess the contamination, we created the virus detection software, VirDetect. detial
FigTree FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST. detial
DNAMAN DNAMAN is a one-for-all software package for molecular biology applications. This package provides an integrated system with versatile functions for high efficiency sequence analysis. You no longer need one program for restriction analyses and others for multiple sequence alignment, designing PCR primers, protein sequence analysis or drawing plasmids ... DNAMAN carries out all these tasks for you. detial
Blast The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. detial
MEGA MEGA can be used with either a graphical user interface (useful for visual exploration of data and results) or a command-line interface (useful for batch or scripted execution). The graphical user interface (GUI) is run in one of two modes. The first mode is the Analyze mode in which all GUI tools in MEGA are enabled and visual results explorers are available for tasks such as editing sequence alignments and viewing phylogenies. This is the mode that most MEGA users are familiar with. The second mode is the Prototype mode which is used solely for generating MEGA Analysis Options (.mao) files that specify analysis settings when using MEGA from a command shell The command-line interface of MEGA is accessed by opening a command shell and executing the megacc command. The megacc command requires several options, including the path to a .mao file and paths to input data file(s) to be analyzed detial
Clustal Clustal 2 comes in two flavors: the command-line version Clustal W and the graphical version Clustal X. Precompiled executables for Linux, Mac OS X and Windows (incl. XP and Vista) of the most recent version (currently 2.1)?along with the source code are?available for download here. You can also?browse for older versions?(Clustal W 1.81, Clustal V etc). detial