Dear Maryam,

You may use PharmDock: a pharmacophore-based docking program.

For more on this program, please see the following link:

https://jcheminf.springeropen.com/articles/10.1186/1758-2946-6-14

or BIOVIA -Pharmacophore and Ligand-Based Design

http://accelrys.com/products/collaborative-science/biovia-discovery-studio/pharmacophore-and-ligand-based-design.html

In addition, attached please find a publication which describes the available softwares for performing a kind of calculations you have mentioned.

Hoping this will be helpful,

Rafik

check the below list with details: https://www.click2drug.org/directory_LigandBasedScreening.html

Pharmer. Free open source pharmacophore search technology that can search millions of chemical structures in seconds.

Catalyst. Pharmacophore Modeling and Analysis; 3D database building and searching; Ligand conformer generation and analysis tools; Geometric, descriptor-based querying; Shape-based screening. Distributed by Accelrys as part of Discovery Studio.

PharmaGist. Freely available web server for pharmacophore detection. The download version includes virtual screening capability.

LiSiCA. LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly. A PyMol plu-in is freely available, too. Developed by the University of Ljubljana, Slovenia.

LigandScout. Fully integrated platform for virtual screening based on 3D chemical feature pharmacophore models. Developed by inte:ligand.

ACPC. (AutoCorrelation of Partial Charges) Open source tool for ligand-based virtual screening using autocorrelation of partial charges. ACPC uses a rotation-translation invariant molecular descriptor.

ChemCom. a computer application which facilitates searching and comparing chemical libraries. ChemCom aims to expedite the current, time consuming processes of comparing large, chemical databases. As such, this application can be used to speedup many processes including drug research and discovery. A free java web application is also available. Developed by the University of Kansas, USA.

MedChem Studio. Cheminformatics platform for computational and medicinal chemists supporting lead identification and optimization, in silico ligand based design, and clustering/classifying of compound libraries. It is integrated with MedChem Designer and ADMET Predictor. Distributed by Simulation Plus, Inc.

PyRX. Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and visualization engine that are essential for Rational Drug Design. AutoDock 4 and AutoDock Vina are used as a docking software. Free and open source. For Windows, Linux and Mac OSX.

Screen Suite. Ligand-based screening tool using fingerprints, 2D and 3D descriptors. Distributed by ChemAxon.

MolSign. Program for pharmacophore identification and modeling. Can be used for querying databases as a pharmacophore based search. Provided by VLife.

Spectrophores. Converts three-dimensional molecular property data (electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials) into one-dimensional spectra independent of the position and orientation of the molecule. It can be used to search for similar molecules and screen databases of small molecules. Open source software developed by Silicos.

Shape-it. free open source shape-based alignment tool by representing molecules as a set of atomic Gaussians. Open source software developed by Silicos.

Align-it. (Formerly Pharao). Pharmacophore-based tool to align small molecules. The tool is based on the concept of modeling pharmacophoric features by Gaussian 3D volumes instead of the more common point or sphere representations. The smooth nature of these continuous functions has a beneficent effect on the optimisation problem introduced during alignment. Open source software developed by Silicos.

Open3DALIGN. Command-line tool aimed at unsupervised molecular alignment. Alignments are computed in an atom-based fashion (by means of a novel algorithm inspired to the LAMDA algorithm by Richmond and co-workers), in a pharmacophore-based fashion using Pharao as the alignment engine, or finally using a combination of the latter two methods. Free open source software. For Windows, Linux and Mac.

GMA (Graph based Molecular Alignment). Combined 2D/3D approach for the fast superposition of flexible chemical structures. Part of the Chil2 suite. Open for general research.

Fuzzee. Allows the identification of functionally similar molecules, based upon functional and structural groups or fragments. Part of the Chil2 suite. Open for general research.

REDUCE. (Formerly FILTER). Tool to filter compounds from libraries using descriptors and functional groups. Part of the Molecular FORECASTER package, from Molecular Forecaster Inc.

SELECT. (Selection and Extraction of Libraries Employing Clustering Techniques). Creates subset of libraries by diversity or similarity using clustering techniques. Part of the Molecular FORECASTER package.

AutoclickChem. Computer program capable of performing click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compounds for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Exists as a web server. Distributed by the National Biomedical Computation Resource.

REACTOR. (Rapid Enumeration by Automated Combinatorial Tool and Organic Reactions). Creates library of molecules by combining fragment libraries from a defined reaction, or from a generic attachment point on the fragments. Part of the Molecular FORECASTER package.

FLAP. (Fingerprints for Ligands and Proteins). Provides a common reference framework for comparing molecules, using GRID Molecular Interaction Fields (MIFs). The fingerprints are characterised by quadruplets of pharmacophoric features and can be used for ligand-ligand, ligand-receptor, and receptor-receptor comparison. In addition, the quadruplets can be used to align molecules, and a more detailed comparison of the GRID MIF overlap calculated. When the template is a ligand, this enables ligand-based virtual screening and alignment. When the template is a receptor site, this enables structure-based screening and pose prediction. Provided by Molecular Discovery.

GASP. Genetic Algorithm Similarity Program. Generates pharmacophores using a genetic algorithm. Distributed by Tripos.

Tuplets. Pharmacophore-based virtual screening. Distributed by Tripos.

KeyRecep. Estimates the characteristics of the binding site of the target protein by superposing multiple active compounds in 3D space so that the physicochemical properties of the compounds match maximally with each other. Can be used to estimate activities and vHTS. Distributed by IMMD.

CATS. Chemically Advanced Template Search. Topological pharmacophore descriptor for scaffold-hopping, screening compound selection and focused library profiling. Developed by the Swiss Federal Institute of Technology Zurich (ETHZ).

u can use pharmmapper or ligand scout (trial version)