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Services


Procurement and sourcing services

Here at Chemspace we understand how important for research and scientific organizations to keep their operations properly supplied and we are ready to take these responsibilities upon ourselves. Our experienced sourcing managers will help you with:

  • Management of multiple suppliers;
  • Sourcing and ordering the compounds and services;
  • Logistic and formatting support including consolidation of samples from different suppliers;
  • Spend management and data analysis;
  • Customer service support.

We will run the whole process of purchasing from the quotation stage to delivery, including resolution of any issues occurred.

 

For our customers’ convenience we offer the following programs:

Procurement and sourcing services (FTE-based):

  • Development of sourcing strategies managing multiple suppliers;
  • Selection and evaluation of suppliers and maintenance of contracts;
  • Sourcing and ordering compounds and services, order management, logistic.

 

Sourcing Building Blocks, reagents, and screening compounds (FFS-based):

  • Multiple suppliers;
  • Transparent price policy;
  • Logistics support.

 

Support of virtual screening programs:

  • Selection from a catalog of 6.5M off-the-shelf compounds from renown trusted suppliers;
  • Fast turnaround;
  • Fixed price.

 

Library design and acquisition:

  • Various chemoinformatic/molecular modeling approaches;
  • Different formatting options, quality control;
  • Hit re-supply.

Library Design

Chemspace's Delivering Discovery Solutions™  offers library design to help researchers identify new hits and improve hit rates in HTS campaigns.

We propose flexible collaboration business models tailored to meet all your needs and budget.

Delivering Discovery Solutions™ in library design has three main approaches:

  • Cheminformatics approach. We use key molecular and structural features, such as molecular weight, hydrogen bond donors/acceptors, etc., to design diversity-oriented libraries, drug-like libraries, lead-like libraries, fragment libraries, - among many others.
  • Target-based approach. With 3D structural information about a particular biological target or family of targets, we can use molecular docking to predict the binding affinity of the putative ligands. This makes the above virtual screening approach one of the most powerful techniques to “cherry-pick” the most promising compounds out of a billion-sized Chemspace catalog.
  • Ligand-based approach. When 3D structures of a particular biological target are unavailable, we can design a focused library based on the known binders. The most common methods of generating ligand-focused libraries are:
  • Search for similar chemical structures of the known active chemical scaffold
  • Using privileged structures
  • 3D ligand pharmacophore model.

 

Why choose Chemspace’s Delivering Discovery Solutions™

  • Large catalog of in-stock small molecules with a diverse offer of chemistry
  • The largest catalog of make-on-demand molecules that are indeed delivered!
  • Experienced team with access to modern software for virtual screens
  • Assistance with SAR, hit-to-lead, and lead optimization studies
  • Expertise in medicinal and organic chemistry.

 

Chemspace's Delivering Discovery Solutions™ provides library synthesis through our valuable chemistry partners to support drug discovery projects. We offer flexible collaboration business models to meet your requirements and fit your budget expectations.

Common library synthesis models:

  • Scaffold-based library. A scaffold provided by either Chemspace or a customer is decorated with a diverse set of building blocks.
  • Make-on-demand analogs. Compounds for a library will be selected from Enamine Real Space.
  • Custom Library. A library designed by a customer.

 

Why choose Chemspace’s Delivering Discovery Solutions™

  • Reliable chemistry partners with expertise in various types of modern chemistry
  • Parallel chemistry, over 100 transformations
  • Flask chemistry, all modern techniques and approaches
  • Access to various scaffolds and decorators (synthetic and natural products)
  • HPLC purification, purity of 90%+
  • Analytical support for synthetic work (HPLC, LC/MS, NMR, and other methods)
  • Preferred formatting and flexible delivery options.

 

Please contact us at info@chem-space.com for more information. Enjoy one of the best services delivered by custom synthesis companies!

Custom Synthesis

Chemspace's Delivering Discovery Solutions™ provide custom synthetic chemistry services for our customers to improve their chemistry effort. We offer flexible business models for the collaboration tailored to your needs and budget.

Delivering Discovery Solutions™ include:

  • High-quality production
  • Fast turnaround time due to the next day access to the largest building blocks collection in the world
  • Synthetic route development toward novel compounds
  • Dedicated project management by business and science professionals; project strategy development
  • Work with your molecular design or you can choose from over 100 million available tractable designs
  • Computational chemistry and CADD
  • Flexible delivery options anywhere over the world

 

Our expertise covers:

  • All possible techniques of modern organic chemistry
  • Organometallic chemistry
  • Multi-step synthesis
  • Heterocyclic chemistry
  • Chiral chemistry including separation of enantiomers and chiral purification
  • Multicomponent reactions (MCR)
  • Custom peptide synthesis including peptidomimetics with non-natural amino acids
  • Macrocyclic synthesis
  • High-Pressure reactions
  • Analytical support for synthetic work (HPLC, LCMS, multinuclear NMR and other methods)

Please contact us at info@chem-space.com for more information. Enjoy one of the best services delivered by custom synthesis companies!

Chemspace KNIME Node

KNIME Analytics Platform is a powerful open source tool for data mining. We have created the Chemspace node for KNIME that allow to search directly in Chemspace database (1.3 billion compounds) without using your browser.

The node allows for search in all database sections at the same time or in any of them separately.

You can embed Chemspace node into your custom in-house workflow, get the information on marketed compounds and post-process the search results in any desired way.

To use the node, you will need the Chemspace API Key that we will send via email. Contact us at info@chem-space.com to request the Key.

You can get up to 2000 results per each query performing up to 40 requests per minute.

What should be the input?

The node accepts SMILES cells (or String cells with SMILES) for Structure Search and String/numeric cells for ID Search.

What is the output?

For each query where results are found, the nodes generate output with SMILES, Chemspace IDs, and URLs.

Also there is an option to show pre-calculated PhysChem parameters for hits.

How to use the node?

Access to Chemspace database from KNIME interface is provided for free, but the API Key is needed. Please follow the instructions below to get the Key:

  1. Register on Chemspace website
  2. Email us on info@chem-space.com with Key request and provide us with your username or email used for registration
  3. Get the Key and explore the chemical universe!

Please see our presentation on Chemspace Search node to explore the features of it!

How to install Chemspace Search nodes?

  1. Launch KNIME.
  2. Open Help menu and click Install New Software.

  3. Type https://chem-space.com/knime/ into the Work with field.

  4. Tick the Chemspace KNIME nodes checkbox.

  5. Click next and follow the further instructions.
  6. For changes to take effect, you will need to restart KNIME. When the installation is complete, the application will propose you to restart it.
  7. You can find Chemspace nodes in your Node Repository after the restart

Computational Services

Analogs Searching

Searching for Analogs

Chemspace professionals are ready to help you with searching for compound analogs using 2D fingerprints (ECFP, FCFP, MACC Keys, etc) and/or 3D shape comparison (Electroshape, USRCAT, E3FP). Manual analogs selection is proven to give much more accurate results than the automatic approaches.
We guarantee confidentiality and quality of obtained data.

Molecular Descriptors and Filters

Applying Molecular Descriptors and Structure Filters on large datasets drastically increases the chance to find the desired sets of compounds with selected properties. This helps you to focus on the valuable chemical space for your research.

Download
Molecular Descriptors and Filters
Molecular Docking

Molecular Docking

Molecular Docking is an efficient method for protein-ligand interactions analysis and screening of large compound libraries against a target protein. It helps to discover biologically active compounds with diverse chemotypes and strong binding affinity.

Download

Molecular Dynamics

Molecular Dynamics methods demonstrate the evolution of the biological system in time. It processes target-drug interaction on a deep level, facilitating the confirmation of selected hits from virtual screening. The estimation of protein-ligand binding energy provided by this method tends to be more accurate.

Download
Molecular Dynamics
QSAR

QSAR

We offer:

  • estimation of physicochemical properties and biological activity
  • prediction of the full activity profile of the given compound against a panel of different biological targets, leading to the development of target profiling and target fishing applications
  • establishment of structure-activity relationships
Download

Virtual screening

Virtual Screening comes into play when you are dealing with huge datasets. Retaining prediction accuracy is the defining factor for screening workflow creation. Our team utilizes in-house modifications of this approach to provide high-quality results of large databases screening. We work with each case exclusively, elaborating the algorithm to obtain the best compound sets.

Download
Virtual screening
Collaborations

Collaborations

We are interested in collaborations as research involving coordination between the researchers, institutions, and/or organizations on win-win conditions. This cooperation can bring distinct expertise to a project. Our computational services can be an important contribution to drug research. Conditions are discussed individually on request.

Sounds interesting? Drop us a line: cs_modeling@chem-space.com

Building Blocks for Library Synthesis

Synthesis of a compound library is an important step prior to wet screening, but it can also become a very costly process. Of course, you can purchase compounds from our Screening Compounds Collection, but what if you want something more specific?

Ordering building blocks in gram quantities for such purposes can be very expensive, but we've got your back!

Chemspace offers a very useful service – Building Blocks for Library Synthesis.

  • It is a collection of 190K compounds from 4 different suppliers, that you can choose from.
  • Compounds are supplied in umol quantities
  • The order will be delivered to you in 1-2 weeks.
  • Customized formatting of your choice (vials, plates, etc.)
  • Consolidated shipments for your best experience

This approach works great for conducting reactions because compounds are shipped pre-weighted in vials. This means that you'll only have to add other components and enjoy the result. A great time saver too!

Contact us at info@chem-space.com for more information.

3D Chemical Spaces

Two of our most popular Screening Compounds Chemical Spaces are available through Molsoft (https://molsoft.com/addons/conf/) as sets of generated 3D structures.

You can download the sets by using the links below:

  • Chemspace Freedom Space (160M compounds)
https://molsoft.com/addons/conf/Chemspace_FreedomConf.molt
  • Chemspace Screening Set (3.9M in-stock compounds)
https://molsoft.com/addons/conf/chemspace_screening_set_conf.molt

These sets are meant to save your time by providing you with already generated 3D structures for computational purposes. We are trying to do our best to be present on different platforms and provide the most easy-to-use products.

For questions drop us a line at info@chem-space.com

3D Chemical Spaces

Punchout Integration

If you frequently use our website, we have a great option for your convenience as a buyer - Punchout Site!

This means you get the chem-space.com website customized to your needs and preferences, and it will be connected to your in-house Purchasing system.

Chemspace Punchout site:

  • Is totally secure.
  • Is 100% customizable (catalogs, discounts, checkout stage, etc.).
  • Includes a personal cabinet for tracking your purchases.
  • Is compatible with any ERP (like Ariba, Coupa, SAP) system by using cXML or Oracle Business Network file data-transfer protocols.
  • Has an automated PO and Invoice transfer data system.
  • Has a full technical support from our experienced IT development team.
  • Has been successfully launched at 15 locations (big pharma, mid and small biotech). And our clients enjoy using it!

We understand that you might have your in-house catalog(s) and we can add them as a separate searchable location that you can select compounds from.

To find out more about the Chemspace Punchout Site, please contact us at info@chem-space.com

Punchout Integration

DEL-ML-CS Approach

A DEL-ML-CS combination speeds up the discovery process

The classical discovery of small molecule therapeutics is an expensive and long process
(https://link.springer.com/article/10.1007/s40273-021-01065-y).

Machine Learning (ML) guided drug discovery is an approach that people came up with to save time and money. But there is a problem – to achieve good results the model must be trained properly. This requires a huge amount of data obtained under the same or close conditions.

We at Chemspace decided to implement the idea, proposed by Kevin McCloskey et al.
(https://pubs.acs.org/doi/10.1021/acs.jmedchem.0c00452) – to combine ML and DNA-encoded libraries (DEL) screens.

Using a DEL screen, it is possible to access quite a big chemical space in a single experiment. This helps to get substantial amounts of data faster and with much fewer resources required. This data can be further used to build an ML model. Application of such a model to ultra-large chemical space of small molecules provided by Chemspace (CS) allows identifying potent hits from the first screen.

So, this combined DEL-ML-CS approach might not only facilitate early drug discovery but also save thousands of dollars.


We at Chemspace, have all the opportunities for you to utilize this approach in your projects. We offer:

  • Access to OpenDEL by HitGen;
  • DEL screening services;
  • ML services;
  • Sourcing from the largest compound catalog;
  • Hit expansion and follow-up.

If you are interested in this opportunity or have any questions, feel free to contact us at info@chem-space.com

DEL-ML-CS Approach