Search Results for "receptor-ligand"
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Showing 42 open source projects for "receptor-ligand"
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nichenetr
NicheNet: predict active ligand-target links between interacting cells
...The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. This model of prior information on potential ligand-target links can then be used to infer active ligand-target links between interacting cells. NicheNet prioritizes ligands according to their activity (i.e., how well they predict observed changes in gene expression in the receiver cell) and looks for affected targets with high potential to be regulated by these prioritized ligands. -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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Protenix
A trainable PyTorch reproduction of AlphaFold 3
Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as... -
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AutoDockParser
A tool for efficient processing of Docking results
...AutoDock Parser offers automatic post-processing of the docking results obtained from AutoDock Suit. AutoDock Parser is a user-friendly tool aimed to minimize the efforts in the post-processing of docking results. It enables the user to create protein-ligand complexes from the input DLG/PDBQT files in a single step. -
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APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.
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Docking-Affinity-Plotter
Docking Affinity Plotter: Visualize and analyze binding affinity data.
...This desktop GUI tool allows researchers to load docking results, generate insightful plots, and create a PDF report. Features ✅ CSV File Loading: Accepts docking results with ligand names, binding affinity, RMSD upper bound (rmsd/ub), and RMSD lower bound (rmsd/lb). ✅ Binding affinity distribution ✅ Density plot of binding affinity ✅ Box plot of binding affinity ✅ RMSD distribution (ub & lb) ✅ 3D scatter plot: Binding affinity vs RMSD ✅ Scatter plots: Affinity vs RMSD ub/lb ✅ Pairwise relationships among affinity and RMSD values ✅ Top 10 ligands by minimum binding affinity ✅ Top 3 recommended ligands ✅ Statistical analysis Citation If you use Docking Affinity Plotter in your research, please cite it as: Md. ... -
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SPINA
Structure parameter inference approach for endocrine feedback control
...A second version has been established for insulin-glucose homeostasis. It delivers the secretory capacity of pancreatic beta cells (SPINA-GBeta), an estimate for the insulin receptor amplification (SPINA-GR) and a static disposition index as a measure for the loop gain of the feedback loop (SPINA-DI). Both implementations of SPINA have been validated in more than 50 clinical studies based on large cohorts. -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1.
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BCI
BCI: Breast Cancer Immunohistochemical Image Generation
...Project pix2pix provides a python script to generate pix2pix training data in the form of pairs of images {A,B}, where A and B are two different depictions of the same underlying scene, these can be pairs {HE, IHC}. Then we can learn to translate A(HE images) to B(IHC images). The evaluation of human epidermal growth factor receptor 2 (HER2) expression is essential to formulate a precise treatment for breast cancer. The routine evaluation of HER2 is conducted with immunohistochemical techniques (IHC), which is very expensive. Therefore, for the first time, we propose a breast cancer immunohistochemical (BCI) benchmark attempting to synthesize IHC data directly with the paired hematoxylin and eosin (HE) stained images. -
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DSF fitting
Python code to fit DSF (ThermoFluor) data
This program uses isothermal analysis to extract binding constants from thermal unfolding data collected at multiple ligand concentrations. -
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DockStream
A Docking Wrapper to Enhance De Novo Molecular Design
DockStream is a docking wrapper providing access to a collection of ligand embedders and docking backends. Docking execution and post hoc analysis can be automated via the benchmarking and analysis workflow. The flexilibity to specifiy a large variety of docking configurations allows tailored protocols for diverse end applications. DockStream can also parallelize docking across CPU cores, increasing throughput. -
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GWOVina 1.0
The Hybrid Grey Wolf Optimization for Protein-Ligand Docking
Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein. Based on the implementation of AutoDock Vina, GWOVina employs grey wolf optimization (GWO) algorithm to speed up the search for optimal ligand poses. Our rigid docking experiments show that GWOVina has enhanced exploration capability leading to significant speedup in the search while maintaining comparable binding pose prediction accuracy to AutoDock Vina. ... -
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POVME (POcket Volume MEasurer) is a program for calculating the volumes of macromolecular (e.g. protein) binding pockets. In essence, POVME floods a pocket-encompassing region with equidistant points, removes those points that are near receptor atoms, and calculates the volume from the remaining points. NOTE: The latest version of POVME is now available at http://git.durrantlab.com/jdurrant/POVME. Versions on SourceForge are not up to date.
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PSOVina 2.0
The Hybrid Particle Swarm Optimization for Protein-Ligand Docking
A fast docking tool based on the efficient optimization algorithm of Particle Swarm Intelligence and the framework of AutoDock Vina. Based on the initial PSO implementation, our PSOVina method has undergone several important improvements to enhance the docking accuary and achieve remarkable efficiency as compared to the original AutoDock Vina. https://cbbio.online/software/psovina/index.html -
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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gaussianfinder
Cavity Detection Program
Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. ... -
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DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.
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irayMol
Molecular visualization
Analyses and Interactive visualizations of the structures, functions and actions of biomolecules including molecular surface computation, and protein-ligand interface and protein-ligand docking where the ligand could a small compound, a nucleic acid, membrane and other proteins, written in C++/Qt/openGL/GLSL with more than 125,000 lines of codes. In addition to Qt, the only external library needed is GSL everything else is coded from the scratch. -
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Blivion
Blivion: BioLayer Interferometry Virus On (only)
Blivion is a software tool for analysing biolayer interferometry measurements of the binding of large vesicles such as influenza virus onto a two-dimensional ligand-coated substrate. -
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ROP : Read origin protocol
ROP is a computational protocol to discover the source of all reads
...The ROP accounts for 98.8% of all reads across poly(A) and ribo-depletion protocols, compared to 83.8% by conventional reference-based protocols. ROP profiles repeats, circRNAs, gene fusions, trans-splicing events, recombined B/T-cell receptor sequences and microbial communities. The ‘dumpster diving’ profile of unmapped reads output by our method is not limited to RNA-Seq technology and may be applied to whole-exome and whole-genome sequencing. For more details see: https://sergheimangul.wordpress.com/rop/ ROP Tutorial: https://github.com/smangul1/rop/wiki -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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(NCS) NEQUIM Contact System
Tool for analyze of interactions in ligand-protein complexes
NEQUIM Contact System (NCS) is a system to generate and analyze interaction vectors of protein-ligand complexes. Core features include multiple views of vectors, multiple selection options, cluster analysis and generation of interaction vector model. The input could be from PDB format or from files generated by automatic docking softwares AutoDock/Vina or Surflex. -
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IL1R TILRR FlameGPU
Agent based model of IL1R1 signalling for FLAME GPU
Agent based model of IL1R1 signalling pathway including the co-receptor TILRR. Model File and Functions file for use with FLAME GPU. Example 0.xml starting iteration file included. -
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binana
BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyz
BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyzing ligand binding. The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions. As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools. As output, BINANA describes ligand binding. -
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DAT_Analyzer
striatal subregional analysis tool for dopamine transporter PET
...DANA utilizes coregistration and spatial normalization functions in SPM8 and therefore requires MATLAB 7.1 (or higher) and SPM8 in 64bit environment with more than 8 GB RAM. MAC OSX OS is recommended. It includes various custom templates for conventional MR, DARTEL MR, two type of CT, and ligand specific PET and also includes various types of striatal subregional VOI templates. It supports five types of spatial normalization methods. (This project will be uploaded soon. It's now under construction.)
