Discovery Studio

Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systèmes BIOVIA (formerly Accelrys).

The product suite has a strong academic collaboration programme, supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including Chemistry at Harvard Macromolecular Mechanics (CHARMM), MODELLER, DelPhi, ZDOCK, DMol3, and more.

Scope

Discovery Studio provides software applications covering the following areas:

Simulations
- Including molecular mechanics, molecular dynamics, quantum mechanics
- For molecular mechanics based simulations: Include implicit and explicit-based solvent models and membrane models
- Also includes the ability to perform hybrid quantum mechanics/molecular mechanics (QM/MM) calculations
Ligand design
- Including tools for enumerating molecular libraries and library optimization
Pharmacophore modeling
- Including creation, validation and virtual screening
Structure-based design
- Including tools for fragment-based placement and refinement, receptor-ligand docking and pose refinement, de novo design
Macromolecule design and validation
Macromolecule engineering
- Specialist tools for protein-protein docking
- Specialist tools for Antibody design and optimization
- Specialist tools for membrane-bound proteins, including GPCRs
QSAR
- Covering methods such as multiple linear regression, partial least squares, recursive partitioning, Genetic Function approximation and 3D field-based QSAR
ADME
Predictive toxicity

References

↑ "BIOVIA". Dassault Systèmes. August 11, 2023.
↑ "List of key Accelrys academic collaborators". Accelrys.com. Archived from the original on November 25, 2011.
↑ Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009-07-30). "CHARMM: The biomolecular simulation program" (PDF). Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. ISSN 0192-8651. PMC 2810661. PMID 19444816.
↑ Webb, Benjamin; Sali, Andrej (2016). "Comparative Protein Structure Modeling Using MODELLER". Current Protocols in Bioinformatics. 54 (1). Supplement 15, 5.6.1-5.6.30. doi:10.1002/cpbi.3. ISSN 1934-3396. PMC 5031415. PMID 27322406.
↑ Rocchia, W.; Alexov, E.; Honig, B. (2001-07-01). "Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions". The Journal of Physical Chemistry B. 105 (28): 6507–6514. doi:10.1021/jp010454y. ISSN 1520-6106.
↑ Chen, Rong; Li, Li; Weng, Zhiping (2003). "ZDOCK: An initial-stage protein-docking algorithm". Proteins: Structure, Function, and Bioinformatics. 52 (1): 80–87. doi:10.1002/prot.10389. ISSN 0887-3585. PMID 12784371.
↑ Matsuzawa, Nobuyuki; Seto, Jun'etsu; Dixon, David A. (1997-12-01). "Density Functional Theory Predictions of Second-Order Hyperpolarizabilities of Metallocenes". The Journal of Physical Chemistry A. 101 (49): 9391–9398. Bibcode:1997JPCA..101.9391M. doi:10.1021/jp952465v. ISSN 1089-5639.
↑
- Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules" (PDF). The Journal of Chemical Physics. 92 (1). AIP Publishing: 508–517. Bibcode:1990JChPh..92..508D. doi:10.1063/1.458452. ISSN 0021-9606.
- Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach" (PDF). The Journal of Chemical Physics. 94 (11). AIP Publishing: 7245–7250. Bibcode:1991JChPh..94.7245D. doi:10.1063/1.460208. ISSN 0021-9606.
- Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach" (PDF). The Journal of Chemical Physics. 113 (18). AIP Publishing: 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606.
↑ Sutter, Jon; Li, Jiabo; Maynard, Allister J.; Goupil, Anne; Luu, Tien; Nadassy, Katalin (2011). "New Features that Improve the Pharmacophore Tools from Accelrys". Current Computer-Aided Drug Design. 7 (3): 173–180. doi:10.2174/157340911796504305. PMID 21726193.
↑ Luu, Tien T. T.; Malcolm, Noj; Nadassy, Katalin (2011). "Pharmacophore Modeling Methods in Focused Library Selection – Applications in the Context of a New Classification Scheme". Combinatorial Chemistry & High Throughput Screening. 14 (6): 488–499. doi:10.2174/138620711795767820. PMID 21521148.
↑ Haider, Muhammad K.; Bertrand, Hugues-Olivier; Hubbard, Roderick E. (2011-05-23). "Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach". Journal of Chemical Information and Modeling. 51 (5): 1092–1105. doi:10.1021/ci100469n. ISSN 1549-9596. PMID 21528911.
↑ Corradi, Valentina; Mancini, Manuela; Santucci, Maria Alessandra; Carlomagno, Teresa; Sanfelice, Domenico; Mori, Mattia; Vignaroli, Giulia; Falchi, Federico; Manetti, Fabrizio; Radi, Marco; Botta, Maurizio (2011). "Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case". Bioorganic & Medicinal Chemistry Letters. 21 (22). Elsevier BV: 6867–6871. doi:10.1016/j.bmcl.2011.09.011. ISSN 0960-894X. PMID 21962576.
↑ Almagro, Juan C.; Beavers, Mary Pat; Hernandez-Guzman, Francisco; Maier, Johannes; Shaulsky, Jodi; Butenhof, Kenneth; Labute, Paul; Thorsteinson, Nels; Kelly, Kenneth; Teplyakov, Alexey; Luo, Jinquan; Sweet, Raymond; Gilliland, Gary L. (2011). "Antibody modeling assessment". Proteins: Structure, Function, and Bioinformatics. 79 (11): 3050–3066. doi:10.1002/prot.23130. ISSN 0887-3585. PMID 21935986.

External links

Official website, Accelrys.com
Discovery Studio
Supporting free software tools: Discovery Studio Visualizer and ActiveX Controls Archived 2011-11-19 at the Wayback Machine

Recent news articles

BioIT World News article on Discovery Studio Archived 2011-10-07 at the Wayback Machine
BioInform (GenomeWeb)

[1] "BIOVIA". Dassault Systèmes. August 11, 2023.

[2] "List of key Accelrys academic collaborators". Accelrys.com. Archived from the original on November 25, 2011.

[3] Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009-07-30). "CHARMM: The biomolecular simulation program" (PDF). Journal of Computational Chemistry. 30 (10): 1545–1614. doi:10.1002/jcc.21287. ISSN 0192-8651. PMC 2810661. PMID 19444816.

[4] Webb, Benjamin; Sali, Andrej (2016). "Comparative Protein Structure Modeling Using MODELLER". Current Protocols in Bioinformatics. 54 (1). Supplement 15, 5.6.1-5.6.30. doi:10.1002/cpbi.3. ISSN 1934-3396. PMC 5031415. PMID 27322406.

[5] Rocchia, W.; Alexov, E.; Honig, B. (2001-07-01). "Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions". The Journal of Physical Chemistry B. 105 (28): 6507–6514. doi:10.1021/jp010454y. ISSN 1520-6106.

[6] Chen, Rong; Li, Li; Weng, Zhiping (2003). "ZDOCK: An initial-stage protein-docking algorithm". Proteins: Structure, Function, and Bioinformatics. 52 (1): 80–87. doi:10.1002/prot.10389. ISSN 0887-3585. PMID 12784371.

[7] Matsuzawa, Nobuyuki; Seto, Jun'etsu; Dixon, David A. (1997-12-01). "Density Functional Theory Predictions of Second-Order Hyperpolarizabilities of Metallocenes". The Journal of Physical Chemistry A. 101 (49): 9391–9398. Bibcode:1997JPCA..101.9391M. doi:10.1021/jp952465v. ISSN 1089-5639.

[8] 
Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules" (PDF). The Journal of Chemical Physics. 92 (1). AIP Publishing: 508–517. Bibcode:1990JChPh..92..508D. doi:10.1063/1.458452. ISSN 0021-9606.
Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach" (PDF). The Journal of Chemical Physics. 94 (11). AIP Publishing: 7245–7250. Bibcode:1991JChPh..94.7245D. doi:10.1063/1.460208. ISSN 0021-9606.
Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach" (PDF). The Journal of Chemical Physics. 113 (18). AIP Publishing: 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606.

[mw-w] Delley, B. (1990-01-01). "An all-electron numerical method for solving the local density functional for polyatomic molecules" (PDF). The Journal of Chemical Physics. 92 (1). AIP Publishing: 508–517. Bibcode:1990JChPh..92..508D. doi:10.1063/1.458452. ISSN 0021-9606.

[mwAQs] Delley, B. (1991-06-01). "Analytic energy derivatives in the numerical local-density-functional approach" (PDF). The Journal of Chemical Physics. 94 (11). AIP Publishing: 7245–7250. Bibcode:1991JChPh..94.7245D. doi:10.1063/1.460208. ISSN 0021-9606.

[mwARs] Delley, B. (2000-11-08). "From molecules to solids with the DMol3 approach" (PDF). The Journal of Chemical Physics. 113 (18). AIP Publishing: 7756–7764. doi:10.1063/1.1316015. ISSN 0021-9606.

[9] Sutter, Jon; Li, Jiabo; Maynard, Allister J.; Goupil, Anne; Luu, Tien; Nadassy, Katalin (2011). "New Features that Improve the Pharmacophore Tools from Accelrys". Current Computer-Aided Drug Design. 7 (3): 173–180. doi:10.2174/157340911796504305. PMID 21726193.

[10] Luu, Tien T. T.; Malcolm, Noj; Nadassy, Katalin (2011). "Pharmacophore Modeling Methods in Focused Library Selection – Applications in the Context of a New Classification Scheme". Combinatorial Chemistry & High Throughput Screening. 14 (6): 488–499. doi:10.2174/138620711795767820. PMID 21521148.

[11] Haider, Muhammad K.; Bertrand, Hugues-Olivier; Hubbard, Roderick E. (2011-05-23). "Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach". Journal of Chemical Information and Modeling. 51 (5): 1092–1105. doi:10.1021/ci100469n. ISSN 1549-9596. PMID 21528911.

[12] Corradi, Valentina; Mancini, Manuela; Santucci, Maria Alessandra; Carlomagno, Teresa; Sanfelice, Domenico; Mori, Mattia; Vignaroli, Giulia; Falchi, Federico; Manetti, Fabrizio; Radi, Marco; Botta, Maurizio (2011). "Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case". Bioorganic & Medicinal Chemistry Letters. 21 (22). Elsevier BV: 6867–6871. doi:10.1016/j.bmcl.2011.09.011. ISSN 0960-894X. PMID 21962576.

[13] Almagro, Juan C.; Beavers, Mary Pat; Hernandez-Guzman, Francisco; Maier, Johannes; Shaulsky, Jodi; Butenhof, Kenneth; Labute, Paul; Thorsteinson, Nels; Kelly, Kenneth; Teplyakov, Alexey; Luo, Jinquan; Sweet, Raymond; Gilliland, Gary L. (2011). "Antibody modeling assessment". Proteins: Structure, Function, and Bioinformatics. 79 (11): 3050–3066. doi:10.1002/prot.23130. ISSN 0887-3585. PMID 21935986.

Discovery Studio

Scope

See also

References

External links

Recent news articles