| Application in combinatorial drug discovery | Application in combinatorial drug discovery |
| Author Summary | Part of the complexity of drug discovery is the sheer chemical diversity to explore combined to all requirements a compound must meet to become a commercial drug. |
| Conclusion and Outlook | These steps can be part of an iterative drug discovery process that will have immediate use in both the pharmaceutical industry and academia. |
| Introduction | Drug discovery faces important challenges in terms of cost, complexity and the amount of time required to yield promising compounds. |
| Introduction | Hence, drug discovery is a combinatorial problem which, unfortunately, cannot be solved using combinatorial chemistry alone. |
| Introduction | Indeed, this transforms the combinatorial drug discovery problem into an equally hard computational task. |
| Simulation of a drug discovery | Simulation of a drug discovery |
| Author Summary | They can be applied to molecular selection, in vitro evolution process, high throughput screening and virtual screening for drug discovery . |
| Introduction | On the practical side, it is also under intensive investigations in drug discovery and pharmaceutical industry [3]. |
| Summary and Conclusion | For the lead compound search in drug discovery , high specificity is often achieved by increasing the specific hydrophobic interactions between the ligand and the target [20], while high affinity often relies on some crucial interactions such as hydrogen-bonding. |
| Summary and Conclusion | When applies to drug screening, this suggests a multidimensional screening strategy using both affinity and specificity rather than affinity alone in the traditional drug discovery . |
| Z‘A j§;~9.5 9=°a’ o | Remarkably, the comprehensive knowledge of the statistics of affinity distributions in many studies have led to a better understanding of molecular selection [59] , and in vitro evolution process such as combinatorial library panning, SELEX technology exploring the RNA/DNA-ligand interactions [60—64] , and high throughput screening for drug discovery to study the receptors or enzymes binding with the lead compounds [65, 66]. |
| drug discovery. | drug discovery . |
| Author Summary | Description of the “mode-of-action” of a small chemical compound against a protein target is essential for the drug discovery process. |
| Discussion | So far, we have applied the method in an open source drug discovery initiative against Mycobacterium tuberculosis [31] and are currently working in other projects and initiatives. |
| Discussion | Our goal is to encourage open source drug discovery by releasing the method with all the predictions expecting that other researchers can benefit from our work. |
| Introduction | Therefore, identification of all possible targets of a chemical compound is critical in the drug discovery process. |
| Introduction | Annolyze was used in an open source drug discovery initiative against neglected tropical diseases [30] while nAnnoLyze has been applied to a set of anti-tubercular drugs against the M ycobacterium tuberculosis proteome [31]. |