Certara offers predictive science and informatics solutions that enable cross-disciplinary and translational approaches to drug development.

Molecular Modeling and Simulation

Benchware 3D Explorer Features Tour

Learn about state-of-the-art molecular graphics, user-friendly interfaces, and scientific and communication capabilities

Share docking results

PDB structure of Proto-oncogene tyrosine-protein kinase with Compound Ru79256 displayed in Benchware 3D Explorer. The original compound was docked back into the protein binding pocket using Surflex-Dock. Two results poses are shown with the original conformation. The top pose is very close to the original conformation, and the hydrogen bonds between the ligands and protein are shown in dashed ellipsoids representation. The binding site is shown as transparent mesh presentation color coded based on lipophilic potential.

Flexibly align ligands

Benchware 3D Explorer allows users to align small molecule structures flexibly to rigid template molecules. This capability is key to chemists involved in projects for which no protein structure is available as it readily allows users to understand 3D structural similarities of small molecules. The image above displays a flexible alignment of two (2) ligands of HIV Protease.

Explore protein-ligand interactions

PDB structure 1NNY displayed in Benchware 3D Explorer depicts a potent, selective protein tyrosine phosphatase 1B inhibitor. Strong, selective binding of the ligand is achieved through hydrogen bonding and shape complementarity between the ligand and the protein binding site as shown by the juxtaposition of their Connolly surfaces. 3D Explorer allows ligands to be modified in the context of the protein or to align new structures to the bond ligand.

Viewpoints and captions

Benchware 3D Explorer’s viewpoints and associated captioning capability allows users to associate their knowledge and insights to structural data presented in Benchware 3D Explorer. Caption text can be hyperlinked to any selectable object in Benchware 3D Explorer such as molecules, atoms, surfaces, and molecular interactions; as well as external files and web pages. Benchware 3D Explorer’s captions allow straightforward knowledge capture and navigation by subsequent viewers, thereby extracting maximum value from structural information.

Automatic update of Lipinski properties

Lipinski properties (Molecular Weight, logP and numbers of hydrogen bond donors and acceptors) are automatically updated as the user modifies the ligand allowing simulataneous multi-parameter optimization.

PDB structure 1KE7

PDB structure 1KE7 displayed in Benchware 3D Explorer depicts a potent, Oxindole-based CDK2 inhibitor. Hydrogen bonding interactions between the ligand and protein backbone and sidechains are depicted by yellow dashed ovoids whose width denotes the strength of the hydrogen bond. Key hydrophobic pharmacophore sites in the ligand are denoted by meshed spheres.

Integrated Development Environment

Using the Integrated Development Environment (IDE) for VBA, developers can rapidly create custom scripts, interfaces, and applications to address the specific needs of life sciences researchers. Custom-developed, task-based interfaces can shorten end user learning curves and leverage proprietary knowledge for strategic research advantage.

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Benchware 3D Explorer

3D Chemical Visualization and Decision Support

Benchware® 3D Explorer allows life sciences researchers, including non-expert molecular modelers, to make more informed decisions based on 3D molecular visualization.  State-of-the-art molecular graphics, user-friendly interfaces, and scientific and communication capabilities allow researchers to view, share, understand, and experiment with complex molecular data such as protein-ligand crystal structures, docking results, molecular alignments, or other 3D chemical information.

Benchware 3D Explorer's unique combination of features and capabilities allow an organization to develop and deliver applications to their researchers' desktops that positively impact their research decision process.

Key Benefits

  • High quality, comprehensive molecular visualization capabilities allow researchers that are not expert molecular modelers to gain access to vital research information.
  • Provides flexible ligand-ligand alignment and protein-protein alignment capabilities.
  • Allows ready comparison of 3D structural features.
  • Intuitive 3D editor allows new chemical ideas to be created and explored in the context of supporting data prior to actual synthesis.
  • Integration with standard productivity software (Symyx Draw, ChemDraw, PowerPoint) allows researchers to easily enter their ideas and present their results.
  • Macro recording capabilities allow repetitive tasks to be automated. Macro scripts can be shared throughout an organization to ensure consistency of research operations.
  • Hyperlinkable captions provides connected knowledge capture capability.
  • Provides a mechanism for modeling groups to readily share their models and results with chemistry and biology researchers, improving ROI on modeling resources and better supporting chemistry and biology operations.
  • Provides a platform for rapid development and deployment of custom solutions and applications. Custom-developed solutions take advantage of proprietary knowledge and increase the efficiency and effectiveness of end user research.

System Requirements

Benchware 3D Explorer will run on PC hardware running any of the following:

  • Windows 7 (32 or 64 bit)
  • Windows VISTA (32 bit versions only)
  • Windows XP


Minimum system configuration:

  • Pentium III or Athlon 1.0 GHz processor or faster (1.5 GHz recommended)
  • 128 MB of memory (256 MB recommended)
  • 50 MB of free disk space
  • Windows-compatible graphics card

Additional memory and processor speed will provide improved performance.

Hardware-accelerated OpenGL graphics hardware is required for optimal Benchware 3D Explorer performance.

Stereo-in-a-window viewing requires the use of specialized stereo glasses, an emitter, a stereo-capable graphics card, and a high refresh rate monitor (118Hz or better recommended) or use of the Zalman stereo LCD.