Intelligent Pharma
Molecular Modeling Services

Areas of Expertise

  • Molecular Field-Based Modeling



    The structural make-up of a molecule includes its molecular fields, which are similar to a cloud around the molecule. With these fields, the molecule can interact with other macromolecules in a cell and carry out its function. Molecular field based modeling uses the characteristics and position of these fields to achieve objectives such as hit identification and optimization. From this information, pharmacore and QSAR models can be constructed.


    Related services :
    • Determination of mechanisms of action
    • Hit identification
    • Drug Reprofiling
    • Selectivity studies
    • Identification of more synthesizable or scalable compounds
    • Extension of patents
    • Determination & selection of back-ups

    Related tools: MEDEA

  • Ligand-Based Virtual Screening



    Given a set of structurally diverse ligands that bind to a receptor, a model of the receptor can be built. This is known as a pharmacore model. A candidate ligand can then be compared to the pharmacore model to determine whether it is compatible and likely to bind.


    The same results can be obtained using a different strategy by developing logic-based rules describing substructure features and chemical properties related to activity using support vector inductive logic programming. The logic-based features provide insight for medicinal chemists. The support vector machine integrates the features to yield a QSAR, which is then used to screen a database of molecules. This approach is well suited for scaffold hopping to identify novel, active molecules.


    Another approach to ligand-based virtual screening is to use 2D chemical similarity analysis methods to scan a database of molecules against one or more active ligand structures.


    Ligand-based virtual screening can also be done by searching molecules with similar shapes to that of the known actives so that they will fit the target binding site and will be more likely to bind.




    Related services :
    • Determination of mechanisms of action
    • Hit identification
    • Drug Reprofiling
    • Selectivity studies
    • Extension of patents
    • Determination & selection of back-ups
    • Identification of more synthesizable or scalable compounds

    Related tools: PEGASUS and HERCULES

  • Receptor-Based Virtual Screening



    Structure-based virtual screening involves the docking of candidate ligands into a target protein, followed by applying a scoring function to estimate the likelihood that the ligand will bind to the protein with high affinity.


    Related services :
    • Determination of new inhibitors
    • Determination of mechanisms of action
    • Drug Reprofiling
    • Selectivity studies

    Related tools: SELENE

  • Fragment-Based Drug Discovery



    Fragment-based Drug Discovery (FBDD) is used to find lead compounds during the drug discovery process. This method is based on the identification of small chemical fragments that can weakly bind to the biological target, and then growing or combining them to produce a lead with a higher affinity. FBDD is similar to high-throughput screening (HTS). In HTS, libraries with millions of compounds are screened, and nanomolar binding affinities are sought. In contrast, in the early phase of FBDD, libraries with only a few thousand compounds are screened, and millimolar affinities are considered useful.


    Related services
    :
    • Hit identification
    • Determination of new inhibitors
  • Scaffold Hopping



    The goal of scaffold hopping is to discover structurally novel compounds from known active compounds by modifying the central core structure of the molecule. Scaffold hopping is a central task of modern medicinal chemistry with a multitude of techniques. This process has led to the creation of several molecules with chemically different core structures, yet they can bind to the same receptor.


    Related services :
    • Hit identification
    • Drug Reprofiling
    • Extension of patents
    • Identification of more synthesizable or scalable compounds

    Related tools: HERCULES

  • Toxicology Predictions



    Mathematical models can be used to predict toxicity using Quantitative Structure Activity Relationship (QSAR) models. These models use different descriptors to represent physical characteristics of the molecules. Models to predict different types of toxicity are available as well.


    Related services :
    • ADME/Tox prediction
    • Hit to Lead
    • Selectivity studies

    Related tools: MEDEA

  • Protein Design



    Protein design is the rational design of new protein molecules that fold to a target protein structure with the ultimate goal of designing novel functions. Proteins can be designed from scratch (de novo design) or by making calculated variations to a known structure and its sequence (protein redesign). The predicted sequences can be validated experimentally through methods such as peptide synthesis, site-directed mutagenesis, or artificial gene synthesis.


    Related services
    • Determination of mechanisms of action
    • Hit to Lead
    • Selectivity studies

    Related tools: 3rd party software

  • Mathematical Models



    A mathematical model is a description of a system using mathematical concepts. A mathematical model can help explain a system, aid in the study of the effects of different components, and make predictions about behavior.


    Related services:
    • ADME/Tox prediction
    • Hit to Lead
    • Selectivity studies

    Related tools: MEDEA

  • Library Design


    Determining active molecules (hit identification) with experimental screens allows for the testing of thousands of compounds. To ensure good hits for a group of targets, computational tools can be used to design molecular libraries. The selection of the molecules for the database is done with respect to their physio-chemical properties, assuring that the molecules are drug-like, diverse, and represent a large chemical space and their theoretical activity towards a specific group of targets.

    Related services:
    • Hit to Lead
    • Hit identification

    Related tools: 3rd party software

  • Data Mining



    Data mining, an interdisciplinary subfield of computer science, is the computational process of discovering patterns in large sets of data, which involves artificial intelligence, machine learning, statistics, and database systems. The overall goal of this process is to extract information from a data set and transform it for further use. This method involves database and data management, data pre-processing, model and inference considerations, interestingness metrics, complexity considerations, post-processing of discovered structures, visualization, and online updating.


    Related services :
    • Hit to Lead
    • Extraction of biological and chemical patterns

    Related tools: MEDEA



  • QSAR



    Quantitative structure-activity relationship models (QSARs) are regression or classification models used in the chemical and biological sciences and engineering. QSAR regression models relate a set of predictor variables to the potency of the response variable, while classification QSAR models relate the predictor variables to a categorical value of the response variable. In QSAR modeling, the predictors consist of physio-chemical properties or theoretical molecular descriptors; the QSAR response-variable could be a biological activity. QSAR models summarize a supposed relationship between chemical structures and biological activity and predict the activities of new chemicals.


    Related services :
    • ADME/Tox prediction
    • Hit to Lead
    • Selectivity studies

    Related tools: MEDEA

  • Homology Modeling



    Homology modeling, also known as comparative modeling of proteins, refers to the construction of an atomic-resolution model of the target protein from its amino acid sequence and an experimental 3D structure of a homologous protein. Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the given sequence, and on the production of an alignment that maps residue in the query sequence to residue in the known sequence.


    Related services:
    • Determination of mechanisms of action
    • Hit to Lead
    • Selectivity studies

    Related tools: 3rd party software

  • Macromolecular Modeling



    Molecular modeling encompasses all theoretical methods and computational techniques used to mimic the behavior of molecules. These methods are used in computational chemistry, drug design, computational biology, and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies.


    Related services :
    • Determination of mechanisms of action
    • Hit to Lead
    • Selectivity studies

    Related tools: 3rd party software

  • Molecular dynamics



    Molecular dynamics is a computer simulation of physical movement of atoms and molecules in the context of N-body simulation. The atoms and molecules are allowed to interact for a period of time, showing the motion of the atoms. The method was originally conceived within theoretical physics but is applied today mostly in chemical physics, materials science, and the modeling of biomolecules. In biophysics and structural biology, the method is frequently applied for ligand docking, lipid bilayer simulations, homology modeling, and ab initio prediction of protein structures by simulation of the folding of the polypeptide chain from a random coil.


    Related services :
    • Determination of macromolecules structures
    • Allosteric binders
    • Determination of new inhibitors
    • Hit identification
    • Selectivity studies

    Related tools: 3rd party software

  • Quantum Chemistry



    Quantum Chemistry is a branch of chemistry dealing with the application of quantum mechanics laws to chemical systems. Theoretical quantum chemistry, which can also be included in the category of computational chemistry, is useful to understand molecules at the subatomic level and help simulate and model more complicated systems. Quantum chemistry is especially useful for systems that are hard to study by experiment. In these ways, quantum chemists investigate chemical phenomena.


    In reactions, quantum chemistry studies the ground, excited, and transition states of atoms and molecules that occur during chemical reactions.


    Quantum chemical studies also use semi-empirical methods, among others, to deal with time dependent problems. Major goals of quantum chemistry include increasing the accuracy of the results for small molecular systems, creating models to describe molecular behavior, and speeding up experimental work, which increases the computer power (proportional to the number of atoms).




    Related services :
    • Determination of macromolecules structures
    • Definition of reaction pathway
    • Determination of molecular properties

    Related tools: 3rd party software

  • Alanine Scanning



    In molecular biology, alanine scanning is a technique used to determine the contributions of a specific residue to the stability or function of a protein. Alanine is used because of its non-bulky, chemically inert, methyl functional group that mimics the secondary structure preferences that many of the other amino acids possess. This technique can also be used to determine if the side chain of a specific residue plays a significant role in bioactivity and is usually accomplished by site-directed mutagenesis or randomly by creating a PCR library. It is a mature technology that is very widely used in biology, chemistry, and biochemistry. The data can be tested by IR, NMR Spectroscopy, mathematical methods, bioassays, etc.


    Related services :
    • Determination of macromolecules structures
    • Hit identification

    Related tools: 3rd party software