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Binding affinity prediction

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…
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…

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…

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…

eTOX ALLIES
Desktop

eTOX ALLIES Automated pipeLine for Linear Interaction Energy-based Simulations

Predicts ligand-binding free energies. eTOX ALLIES allows unsupervised…

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…

AutoGrow
Desktop

AutoGrow

Optimizes candidate ligands for predicted binding affinity and other druglike…

Optimizes candidate ligands for predicted binding affinity and other druglike properties. AutoGrow attempts to introduce some chemical intuition into the automated optimization process. It uses the…

HYDE
Desktop

HYDE HYdrogen bond and DEhydration energies

Allows users to calculate molecular surface components. HYDE is based on the…

Allows users to calculate molecular surface components. HYDE is based on the estimation of hydrogen bond and dehydration energies emerging during protein–ligand binding. The functions of this tool…

BADock
Web
Desktop

BADock Binding Affinity Dock

Predicts binding energies of protein pairs. BADock relies on the classification…

Predicts binding energies of protein pairs. BADock relies on the classification of structural domains and super-secondary structures where a relevant number of such structural features were located…

mhcPreds
Desktop

mhcPreds

Generates such predictions with accuracy comparable to state-of-the-art…

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…

Dscam1 Web…
Web

Dscam1 Web Server

Predicts Down syndrome cell adhesion molecule (Dscam1) self- and hetero-…

Predicts Down syndrome cell adhesion molecule (Dscam1) self- and hetero- binding affinity for batches of Dscam1 isomers. Dscam1 Web Server helps the study of Dscam1 affinity and helps researchers…

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…

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…

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…

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…

DMKPred
Desktop

DMKPred Drug Molecules for Kinase protein

Calculates binding of chemical molecules with protein kinases. DMKPred is a…

Calculates binding of chemical molecules with protein kinases. DMKPred is a Support Vector Machine (SVM) based webserver for the prediction of binding of chemical molecules with specific kinases. It…

KetoDrug
Web

KetoDrug

Binds affinity prediction of ketoxazole derivatives. KetoDrug is a…

Binds affinity prediction of ketoxazole derivatives. KetoDrug is a user-friendly web server for the prediction of binding affinity of small chemical molecules against Fatty Acid Amide Hydrolase…

autocorrelator
Desktop

autocorrelator

Allows to build model automatically to combine applications in order to form…

Allows to build model automatically to combine applications in order to form computational pipelines. autocorrelator permits to determine the optimum parameters for docking, superposition, and…

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