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g_mmpbsa
Implements the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach using subroutines written in-house or sourced from the GROMACS and APBS packages. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks-Chandler-Andersen like integral method).
CSM-lig
A web server tailored to predict the binding affinity of a protein-small molecule complex, encompassing both protein and small-molecule complementarity in terms of shape and chemistry via graph-based structural signatures. CSM-Lig was trained and evaluated on different releases of the PDBbind databases, achieving a correlation of up to 0.86 on 10-fold cross validation and 0.80 in blind tests, performing as well as or better than other widely used methods. The web server allows users to rapidly and automatically predict binding affinities of collections of structures and assess the interactions made. We believe CSM-lig would be an invaluable tool for helping assess docking poses, the effects of multiple mutations, including insertions, deletions and alternative splicing events, in protein-small molecule affinity, unraveling important aspects that drive protein–compound recognition.
ACFIS / Auto Core Fragment In silico Screening
A web server for fragment-based drug discovery. ACFIS includes three computational modules, PARA GEN, CORE GEN and CAND GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery.
MANORAA / Mapping Analogous Nuclei Onto Residue And Affinity
A web service for identification of ligand & residue interactions, SNP and pathway analysis. Manoraa allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein–ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time.
CaFE / Calculation of Free Energy
An easy-to-use pipeline tool to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. CaFE provides a user-friendly choice for researchers who want to perform a post-molecular dynamic energetic analysis using the end-point methods. It is a VMD plugin written in Tcl and the usage is platform-independent.
MMPBSA.py
A program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations.
eTOX ALLIES / Automated pipeLine for Linear Interaction Energy-based Simulations
Predicts ligand-binding free energies. eTOX ALLIES allows unsupervised protein-ligand binding affnity (free energy) computation using iterative linear interaction energy (LIE) theory. The software can be useful for pharmaceutical scientists, toxicologists and modelers interested in predicting binding affinities toward (of-)targets for which structural features of the binding site and/or thermal conformational effects can significantly affect the ligand-binding process.
FEW / Free Energy Workflow
Facilitates setup and execution of ligand binding free energy calculations with AMBER for multiple ligands. FEW allows setting up three types of free energy calculations that operate at different levels of rigor and computational demand: MM-PB(GB)SA, LIE, and TI calculations. The hierarchical and template-based design makes that FEW requires minimal input information but, at the same time, remains highly adaptable. Thus, the program constitutes a ‘‘gray box’’ and should be of interest to both beginners in the field of free energy calculations and expert users.
mhcPreds
Generates such predictions with accuracy comparable to state-of-the-art methods. mhcPreds is a framework for the development of computational studies targeting novel drug-discovery using a novel approach to protein-protein representation, interaction, and modeling. It is designed to be extensible, hackable, and flexible enough to allow researchers to both use it a tool for generating new predictions from their own sequences, as well as deep learning enthusiasts interested in novel, unexplored applications of such techniques.
YANK
Calculates ligand binding affinities in implicit and explicit solvent. YANK uses a sophisticated set of algorithms to rigorously compute biomolecular ligand binding free energies. It performs an alchemical free energy calculation in either implicit or explicit solvent, in which the interactions between a ligand are decoupled in a number of alchemical intermediates whose interactions with the environment are modified, creating an alternative thermodynamic cycle to the direct dissociation of ligand and target biomolecule.
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