Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can…
MANORAA
Web

MANORAA Mapping Analogous Nuclei Onto Residue And Affinity

A web service for identification of ligand & residue interactions, SNP and…

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…

CSM-lig
Web

CSM-lig

A web server tailored to predict the binding affinity of a protein-small…

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…

CaFE
Desktop

CaFE Calculation of Free Energy

An easy-to-use pipeline tool to conduct MM/PBSA and LIE calculations. Powered…

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…

FEW
Desktop

FEW Free Energy Workflow

Facilitates setup and execution of ligand binding free energy calculations with…

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…

YANK
Desktop

YANK

Calculates ligand binding affinities in implicit and explicit solvent. 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…

cBinderDB
Data

cBinderDB

Provides information on covalent binding compound structures, chemotypes,…

Provides information on covalent binding compound structures, chemotypes, targets, covalent binding types, and other biological properties. cBinderDB is a covalent binder database. The covalent…

ACFIS
Web

ACFIS Auto Core Fragment In silico Screening

A web server for fragment-based drug discovery. ACFIS includes three…

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…

g_mmpbsa
Desktop

g_mmpbsa

Implements the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA)…

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…

MMPBSA.py
Desktop

MMPBSA.py

A program written in Python for streamlining end-state free energy calculations…

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…

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