COSMOsim3D and COSMOsar3D 生命科學軟體-生化統計分析軟體/新永資訊有限公司

COSMOsim3D and COSMOsar3D 生命科學軟體

COSMOsim3D and COSMOsar3D 生命科學軟體

  • COSMOsim3D and COSMOsar3D 生命科學軟體
  • 編號
  • 類別
    生化統計分析軟體
  • 介紹
    The COSMO-RS method has proven the σ-profiles as the crucial information for most ADME properties as solubility, blood-brain-partition coefficients, and intestinal absorption, and even for many adsorption phenomena. Considering this fundamental importance of the σ-profiles for surface interactions of molecules in liquid states, they most likely also carry a large part of information required for the estimation of desolvation and binding processes, which are responsible for the inhibition of enzyme receptors by drug molecules. Thus a high similarity with respect to the σ-profiles appears to be
  • 價格

COSMOsim3D

Based on the fact that ligands similar to an active ligand show an increased probability to be also active, ligand-based drug design does not require a target structure. The art of ligand-based drug design thus consists of finding adequate representations of the intermolecular interaction patterns of ligands defining a meaningful similarity measure. Typically, the similarity between ligand molecules is assessed in terms of two- or three-dimensional structure, shape, polar interactions, and pharmacophoric models.

COSMOsim3D is a unique and very robust method for automatic and unsupervised field-based ligand-ligand alignment and similarity searches. It utilizes local σ-profiles, which have been proved to contain the required information on the relevant molecular interactions.

The molecular surface charge approach of COSMOsim3D naturally enables scaffold hopping. Thus, the COSMOsim3D method is suited for datasets with different chemotypes, allowing users to find alternative chemical scaffolds with similar shape and polar features.

Key features:
  • • Pairwise alignment and similarity assessment: COSMOsim3D utilizes LSPs instead of chemical structure or pharmacophores to assess a molecule’s similarity to a template molecule. This enables scaffold hopping and allows users to deal with datasets of different chemotypes.
  • • Multi-template alignment: It is possible to align multiple template molecules and use their superposition as a virtual template molecule. The virtual template molecule can be used for alignment and similarity assessment of potential ligand molecules.
  • • Ligand-Based virtual screening: COSMOsim3D can be used to rank a set of potential ligand molecules according to their similarity to a single template or a virtual template stemming from the superposition of multiple ligands. Thus, it allows users to enrich ligand sets with potential cognate drugs, generating fewer false positives and more true hits.
 

COSMOsar3D

As an alternative approach to similarity-based ligand assessment, QSAR models are used to correlate computed properties of molecules and their biological activity. COSMOsar3D is an extension of COSMOsim3D which uses the LSPs of aligned ligands as a novel set of molecular interaction fields for 3D-QSAR.

In a recent study, LSP-based COSMOsar3D models instantly had a significantly higher predictivity than standard 3D QSAR models. Utilizing smooth spatial histograms introduces an increased robustness of the models against small geometrical shifts of the ligands relative to the grid even at larger grid spacing. In a histogram, a local property hotspot is smoothly partitioned over the neighboring grid points, resulting in a position-independent representation.

Key features:
  • • Robustness and Predictivity: Instead of using properties directly as input for MFA, COSMOsar3D uses a histogram of a property. This approach leads to very robust performance of the models with respect to grid size, grid position and small misalignments, while retaining increased predictive accuracy.
  • • Ionic and Neutral Molecules: The polarization charge densities of neutral and charged species are in the same range, which allows for the inclusion of compounds of varying charge states in the same model.
  • • Linear Relationship of logKi and LSPs: LSPs constitute an optimally suited set of descriptors for a linear regression analysis of pKi values, according to the 3D-QSAR paradigm. COSMOsar3D provides a rationale that logKi values should be linear functions of the LSP descriptors. To the best of our knowledge, no other set of molecular fields used so far in MFA can claim such a sound theoretical justification for the expectation of a linear pKi model.
  • • Description of Hydrogen Bonding: As shown in a recent paper, the polarization charge densities σ are better suited for the description of hydrogen bonding than the electrostatic potential, which is usually employed in MFA. See also “Polarization charge densities provide a predictive quantification of hydrogen bond energies.”
 

COSMOsim3D & COSMOsar3D

Local σ-profiles
Justified by the general COSMO-RS finding that intermolecular interactions can be excellently quantified based on the COSMO surface polarization densities σ, COSMOsim3D introduces local σ-profiles (LSPs) for the alignment and similarity measure of ligands. LSPs are σ-histograms, resulting from projecting the molecular σ-surface onto a 3D-grid, and they provide information about
  • • electrostatics
  • • hydrogen bonding
  • • hydrophobic interactions
  • • shape
Using LSPs, COSMOsim3D meanwhile has been proven to be a very accurate and extremely robust method for automatic and unsupervised field-based ligand-ligand alignment and similarity searching.
 
 

CrystalDiffract v6 化學分子軟體

CrystalDiffract將X射線和中子粉末衍射的世界帶到您的計算機屏幕上,通過交互式控制和輕鬆表徵您的實驗數據。實時參數控制可讓您試驗衍射和样本設置,並提供即時反饋。將這些與即時混合物創建相結合-以及在同一窗口中加載觀察數據的能力 -您將擁有一個強大的工作台應用程序,供研究人員、教師和學生使用。

CrystalDiffract v6 化學分子軟體

COSMOsim3D and COSMOsar3D 生命科學軟體

The COSMO-RS method has proven the σ-profiles as the crucial information for most ADME properties as solubility, blood-brain-partition coefficients, and intestinal absorption, and even for many adsorption phenomena. Considering this fundamental importance of the σ-profiles for surface interactions of molecules in liquid states, they most likely also carry a large part of information required for the estimation of desolvation and binding processes, which are responsible for the inhibition of enzyme receptors by drug molecules. Thus a high similarity with respect to the σ-profiles appears to be

COSMOsim3D and COSMOsar3D 生命科學軟體

GraphPad Prism 10 生物統計軟體

GraphPad Prism 10 是一款全球知名的科學繪圖和數據分析軟體,幫助研究人員更快、更輕鬆地進行實驗數據分析和呈現。它提供了豐富的分析工具和圖表模板,支持不同領域的數據分析,如生物學、醫學、化學、物理學等。使用GraphPad Prism 10,您可以輕鬆地進行統計分析、曲線擬合、圖表繪製、報告生成等操作。其優秀的圖形設計和易於使用的介面,使您可以輕鬆地將您的研究成果呈現出來。如果您是一名研究人員或學術人員,GraphPad Prism 10是您不可或缺的工具。

GraphPad Prism 10 生物統計軟體