Working with AFFINImeter models based on a stoichiometric equilibria approach

The appropriate design and use of binding models in AFFINImeter pass through an understanding of the nomenclature that the software uses to describe a given experimental setup and the species that take part in the assay.
AFFINImeter contemplates the presence of up to three species participating in the experiment: 1) the titrant, or compound placed in the syringe; 2) the titrate, or compound in the calorimetric cell and 3) a co-solute or third compound that can be in the syringe and/or in the cell. These species are labelled in the reaction builder as follows:

As illustrated in Fig. 1, M always refers to the compound placed in the calorimetric cell and A always refers to the compound in the syringe. B always refers to a third component that can be in the syringe (Fig. 1b), in the cell (Fig. 1c) or in both places at once (Fig. 1d):


Once the nomenclature of  AFFINImeter is clear, you can download this note that our scientific team have prepared to understand how our users can be working with models based on a stoichiometric equilibria approach:


You can also check our latest post where we describe “The concepts of stoichiometric and site binding constants”


AFFINImeter is on sales!


This month we have prepared a special offer just to let you exploit the full potential of AFFINImeter:

 15 % off in our Advanced plans*.

Select the technique AFFINImeter Spectroscopy and/or AFFINImeter ITC.




… Use this coupon in our online shop and get right away your discount!


To use our online shop it will be necessary to have an AFFINImeter account, to create one click here.

AFFINImeter Shop

Or if you prefer we can send you an official quotation, click on the button below:​

Get a Quotation



*The promotion is available until May 31st and applicable for all AFFINImeter Advanced plan (ITC and/or Spectroscopy) which duration is equal or greater 1 year. The advanced account includes Global fitting, access to complex binding models, Kinetic information (KinITC tool available for AFFINImeter ITC), orthogonal approach (Multitechnique analysis available in AFFINImeter Spectroscopy)...




AFFINImeter new version!

Last week we announced a release of our new software: AFFINImeter for Spectroscopic Techniques.  Together with this release, we have also improved several aspects of the AFFINImeter software, see what is new in our new version:

1. As we have already mentioned, in this version included a new technique: Spectroscopy (and all its variants: UV-vis, InfraRed, Fluorescence, Circular Dichroism… among others)

  • Just upload new data, select Spectroscopy technique and follow the wizard to import your data.
  • Data must be uploaded in CSV format.
  • Create projects of Fitting and Global fitting with any model you want.

2. Recent activity shows you the latest modified/created files or projects of any technique


3. Now AFFINImeter will use the maximum width of your screen to show your data/projects, for a better experience using wide-screen monitors.

4. Navigation path visible in all views

Fixed problems:

1. Fixed recursively deleting a folder and its contents

2. More validations while selecting a model for NMR technique (and Spectroscopy also):

  • In NMR and SPEC, you cannot use a model that only contains A in its reactions. Now more here

3. Multiple minor usability improvements and performance tweaks.

4. Multiple bug fixes and issues suggested by our users have been implemented and resolved.


What does it look like to you?

It might look like a plain hat or an elephant being eaten by a boa constrictor, but actually, the shape of this curve looks like a typical spectrum of UV-Vis determined by changes in the intensity of this energy and also it represents the logo of our new software:

AFFINImeter for spectroscopic techniques!


Hence, we want to take this opportunity to launch AFFINImeter Spectroscopy software.

It is a new software for the processing and advanced analysis of binding isotherms obtained from different spectroscopic techniques: 1D-NMR, Uv-vis, fluorescence, circular dichroism, differential scanning fluorimetry…


…and from now on, you will be able to start using it:

Get a free trial

To get started, we have prepared some scientific material as an example of how to use AFFINImeter Spectroscopy:

We have prepared a special offer to celebrate the launch of AFFINImeter for Spectroscopic techniques.
Using this code coupon you will get a 25% off*, to buy through our online shop:


 You can also ask for a quotation here 
*The discount will be applied until 2018/03/03.

Open position: Chief Operating & Financial Officer (COFO)

Founded in 2013, Software 4 Science Developments (S4SD) is a leading cloud computing service provider of scientific software AFFINImeter, with more than 1.000 users including the biggest pharmaceutical corporations and research centres and Universities. The company is headquartered in Santiago de Compostela.

We are looking for a COFO to manage the planning and business functions, as well as the overall operations of the company. In addition to general responsibility for financial planning and controls, personnel administration, systems and physical facilities, the COFO should plan for the changing needs of the organization, share responsibility for strategic planning, practice management, and marketing, and contribute to aligning organizational structure with strategy. The COFO will lead and direct the operational and administrative functions of the firm, including accounting and finance, human resources, facilities, conflicts, and records management. This person will be a member of the firm’s Executive Committee.

The COFO supports to the CEO in:

  • Matters of strategy and business development, coordinating the different areas of the company.
  • Providing strategic support through facilitating or advising strategy development while demonstrating foresight, conceptual capability and environmental market awareness. The COFO should manage the leads acquisition and integration for short and long-term strategy development.
  • Development and management of transverse projects of transformation (digital, organization and processes), ensuring the constant simplification and growth of the business. Management of internal communication related to the transformation activities.
  • Managing the corporate agenda, including the various internal/external committees and boards.
  • Constant relation to Shareholders & Senior Management.

The COFO is responsible for:

  • Finding public and private sources of funding.
  • Financial Management: Including planning, forecasting, budgeting, variance analysis, profitability analysis, financial reporting, general ledger accounting, billing, cash flow control, banking relationships, tax planning, tax reporting, trust accounting, payroll, and other financial management functions.
  • Human Resource Management: Including recruiting, selection, training and development, performance evaluation, budgeting and salary administration, employee relations, benefits administration, workers’ compensation, job design and other human resource management functions.
  • Systems Management: Participation in the design and implementation of a KPI information system for all areas of the company, operational audits, cost/benefit analysis, information services, document management systems and procedures, information storage and retrieval, litigation support, and other systems management functions.

Required skills:

  • Bachelor’s degree and preferably an MBA
  • 8+ years of experience, 3+ in a senior position as a Chief Operational Officer and/or Chief Financial Officer, preferably in software companies and/or startup environments.
  • Competencies skills: Used to working in international environments. Results-oriented, strategic thinker and planner. Teamwork. Communication and interpersonal skills. Synthesis and presentation skills. Time management and ability to prioritize. Hands-on proactive attitude. Analytical. Creativity. Proficiency in English / Native Spanish

We offer:

  • Salary: based on interview, bonuses
  • Real ownership and results
  • And a competitive, friendly, international team!

Please contact to

AFFINImeter Spectroscopy


Is a new software for the advanced analysis of isotherms obtained by spectroscopic techniques, such as Uv-vis, circular dichroism, fluorescence… among others, to calculate binding constants.
We are pleased to announce that we are going to release very soon a beta version of AFFINImeter Spectroscopy. That is why we would like to invite you to become one of our beta testers, just click on the button below!

I want to become a beta tester!



I want to become a beta tester!

Global fitting: the key for a robust analysis

Download use case: Global Fitting


The Indian parable of “The six blind men and the elephant” tells the story of six blind men who touch an elephant in the hope of learning what it is like. As each one can only feel a different part of the animal the individual conclusions obtained are in disagreement and none of them provides a real view of the full elephant. “only by sharing what each of you knows can you possibly reach a true understanding”; that´s the moral behind this nice story.


Fig 1: The six blind men and the elephant: only a global analysis of the overall data provides a true understanding.

The binding assay(s) achieved to characterize a molecular interaction often provides not just one, but several binding curves from which the affinity constant is obtained.
Sometimes, an individual fit of these curves yield a set of binding constants that are significantly different from them; this result can be very confusing because, in principle, these binding curves are a representation of the same binding event and should converge to provide the analogous information. Often, the explanation for this behaviour is that the different curves indeed provide only partial and/or different information of the interaction, not enough to unequivocally determine the binding affinity through individual analysis.

“It´s like feeling only a separate part of the elephant”

This is a typical scenario when facing the study of complex binding events that involve more than one equilibrium and several binding curves are obtained, i.e. from different frequencies of the spectra in a titration experiment, from data registered using different techniques (ITC, NMR, Optical Spectroscopies…) and/or from experiments performed at different concentrations of the species participating in the binding event.

Analogous to the parable of the six men and the elephant, the way to get a true understanding of the binding event consist of the global analysis of the different curves.

Fig 2: The binding curve obtained from 2D NMR titrations.

Being aware of the relevance of global analysis, in AFFINImeter we count with the possibility to perform Global fitting of multiple data to tailored binding models where one or more fitting parameters are shared between isotherms. The number and identity of the parameters shared are selected by the user.
Moreover, two or more parameters can be related through mathematical relationships designed by the user. All these features make our global fitting tool the most potent among others to perform a robust analysis of binding data of complex interactions.

About the disuses of  Isothermal Titration Calorimetry in drug discovery research

Isothermal Titration Calorimetry (ITC) is the gold standard for the calculation of affinity in molecular interactions. Many times, researchers claim that the high consumption of sample does not offset the use of ITC for Kd calculation.
Conversely, ITC hides many surprises in the acquisition data that can provide more information in a single experiment that other techniques that are more expensive and more complicated to use.

Download the PDF file of Implementation of kinITC into AFFINImeter


1. ITC collects data from the interaction as a function of time that can be analyzed to obtain kinetic information (kon and koff values). It can cover a very similar range as Surface Plasmon Resonance in a “label-free” and “in-solution” manner (Fig 1).

2. ITC can also provide valuable information about the mechanism of interaction. The high sensitivity of the ITC sensor makes it sensitive to more intriguing interactions as conformational changes, cooperativity…

Using a global fitting approach for the analysis of the isotherms and a model builder to create tailored binding models, the different mechanisms of interaction can be confirmed and characterized.

Find attached a couple of publications describing the application of this new method for ITC data analysis:

Download the PDF file of Implementation of kinITC into AFFINImeter


The concepts of stoichiometric and site binding constants

Download: The concepts of stoichiometric and site binding constants

The interaction between a monovalent ligand L and a multivalent receptor R involves the presence of various species, including the complex of R fully saturated with a number of ligands, and intermediate complexes of R partially saturated. This scenario can be described in terms of reaction schemes following two approaches:


  1. Based on equilibria between existing stoichiometric species (Stoichiometric approach).
  2. Based on equilibria between L and specific interaction sites of R (independent sites approach).
For a better understanding, let´s consider a particular case where L binds to a bivalent receptor:

1. Stoichiometric approach

This approach uses reaction schemes based on equilibria between stoichiometric species and yields stoichiometric binding constants. A model based on stoichiometric equilibria is valid to fit data of both independent and non-independent events and therefore, it is of wider applicability.

Here, the reaction scheme includes a first equilibrium between the free species and the intermediate RL and the second equilibrium between RL + L and RL2 (Fig. 1). The corresponding binding constants, K1 and K2, are denominated stoichiometric binding constants since they refer to equilibria between stoichiometric species.

2. Independent site approach

This approach uses a reaction scheme based on the binding of the ligand to individual sites present in the receptor and considering that all the sites are independent; thus, it supplies site binding constants.

In this case, the reaction scheme considers the presence of two sites in the bivalent receptor and two intermediate complexes (R, L and RL) formed when the ligand binds to s1 or s2 and consequently, the existence of a total of 4 equilibria (Fig. 2). The corresponding binding constants, Ks1, Ks2, Ks1s2 and Ks2s1, are denominated site binding constants since they refer to equilibria between L each specific site of R.

If you want to know more about how to get the stoichiometry (number of sites) and site binding constants with the independent sites approach you can click on the following button:


How to get the most out of biophysical techniques to address binding interactions?

The analysis of isotherms is the more direct way to calculate binding constants for molecular interactions. Isotherms can be obtained using different techniques (ITC, SPR, NMR, Uv-vis, IR, Fluorescence, Circular Dichroism…) and at different experimental conditions.


1. The global fitting approach allows to simultaneously analyze several isotherms obtained by different biophysical techniques and/or at different experimental conditions in a very accurate manner.



2. Many interacting systems do not bind with a simple 1:1 model, more complex binding model can be designed to address complex interaction

3. Using tools to globally analyze isotherms obtained by different biophysical techniques is the most reliable method to characterize binding interactions by the orthogonal approach.

Click here to star using AFFINImeter and to start to create your own binding model: