101 Open source projects that are alternatives of or similar to screenlamp

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

🧬 An R package for visualizing molecular data in 3D

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.

Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.

NequIP is a code for building E(3)-equivariant interatomic potentials

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Computational Analysis of Novel Drug Opportunities

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

A curated list of awesome computational cryo-EM methods.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A Curated List of Computational Biology Datasets Suitable for Machine Learning

CPM implementation in pure JavaScript

Quantum Mechanical Bespoke Force Field Derivation Toolkit

active learning for accelerated high-throughput virtual screening

An R Package for Geneset Enrichment Workflows

Collection of scripts for bacterial genomics

Contact map analysis for biomolecules; based on MDTraj

QUICK: A GPU-enabled ab intio quantum chemistry software package

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

The Biochemical Algorithms Library

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

Perl-Speaks-NONMEM

A Python wrapper for PaDEL-Descriptor software

A Software to interactively edit data in a graphical manner

Population Experimental Design (PopED) in R

Syntax highlighting for computational biology

Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Simulate PK-PD models defined as ODE systems

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Spatial alignment of single cell transcriptomic data.

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Advanced Docking System for Qt

GW-BSE for excited state Quantum Chemistry in a Gaussian Orbital basis, electronic spectroscopy with QM/MM, charge and energy dynamics in complex molecular systems

🎉 Simple restricted Hartree-Fock code in Python

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Ultrafast sequence typing and gene detection from NGS raw reads

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".

Deep learning framework for data mining protein-protein interactions using CNN

Probabilistic Inference for NOvel Therapeutics

Web Interface for ChEMBL @ EMBL-EBI

odr.chalmers.se/handle/20.500.12380/256629?locale=en

stda program for computing excited states and response functions via simplified TD-DFT methods (sTDA, sTD-DFT, and SF-sTD-DFT)

An update to Component factory's krypton toolkit to support .NET Framework 4.6.2 - 4.8.1 to .NET Core/.NET

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

The Microbiome Interpretable Temporal Rule Engine

Myokit: A simple interface to cardiac cellular electrophysiology

Periodic table, physical constants, and molecule parsing for quantum chemistry.

A library to build and execute typed scientific workflows

Streamlining SLAM-seq analysis with ultra-high sensitivity

Fitness landscape exploration sandbox for biological sequence design.

Python for chemoinformatics

A PyMOL plugin for visualizing vibrations in molecules and solids

A Go package for engineering organisms.

Clustering scRNAseq by genotypes

MolMap: An Efficient Convolutional Neural Network Based Molecular Deep Learning Tool

Teaching Utility for Classical Atomistic Simulation.