|
1
|
Schlick T, Portillo-Ledesma S, Myers CG, Beljak L, Chen J, Dakhel S, Darling D, Ghosh S, Hall J, Jan M, Liang E, Saju S, Vohr M, Wu C, Xu Y, Xue E. Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field. Annu Rev Biophys 2021; 50:267-301. [PMID: 33606945 PMCID: PMC8105287 DOI: 10.1146/annurev-biophys-091720-102019] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We reassess progress in the field of biomolecular modeling and simulation, following up on our perspective published in 2011. By reviewing metrics for the field's productivity and providing examples of success, we underscore the productive phase of the field, whose short-term expectations were overestimated and long-term effects underestimated. Such successes include prediction of structures and mechanisms; generation of new insights into biomolecular activity; and thriving collaborations between modeling and experimentation, including experiments driven by modeling. We also discuss the impact of field exercises and web games on the field's progress. Overall, we note tremendous success by the biomolecular modeling community in utilization of computer power; improvement in force fields; and development and application of new algorithms, notably machine learning and artificial intelligence. The combined advances are enhancing the accuracy andscope of modeling and simulation, establishing an exemplary discipline where experiment and theory or simulations are full partners.
Collapse
Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, New York, New York 10003, USA;
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
| | | | - Christopher G Myers
- Department of Chemistry, New York University, New York, New York 10003, USA;
| | - Lauren Beljak
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Justin Chen
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sami Dakhel
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Daniel Darling
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sayak Ghosh
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Joseph Hall
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Mikaeel Jan
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Emily Liang
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sera Saju
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Mackenzie Vohr
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Chris Wu
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Yifan Xu
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Eva Xue
- College of Arts and Science, New York University, New York, New York 10003, USA
| |
Collapse
|
|
2
|
Xue E, Tresoldi C, Sala E, Crippa A, Mazzi B, Greco R, Messina C, Carrabba MG, Lupo Stanghellini MT, Marktel S, Corti C, Peccatori J, Bernardi M, Ciceri F, Vago L. Longitudinal qPCR monitoring of nucleophosmin 1 mutations after allogeneic hematopoietic stem cell transplantation to predict AML relapse. Bone Marrow Transplant 2015; 51:466-9. [PMID: 26642331 DOI: 10.1038/bmt.2015.296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- E Xue
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy.,Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - C Tresoldi
- Molecular Hematology Laboratory, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - E Sala
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - A Crippa
- Molecular Hematology Laboratory, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - B Mazzi
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - R Greco
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - C Messina
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - M G Carrabba
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - M T Lupo Stanghellini
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - S Marktel
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - C Corti
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - J Peccatori
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - M Bernardi
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - F Ciceri
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - L Vago
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milano, Italy.,Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| |
Collapse
|
|
3
|
Lin L, Ye Z, Xue E. [Intraoperative ultrasonographic detection of liver metastasis from tumors of the digestive tract]. Zhonghua Zhong Liu Za Zhi 2001; 23:234-6. [PMID: 11783095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To ascertain the value of intraoperative ultrasonography to early detect liver metastasis from tumors of the digestive tract. METHODS Intraoperative ultrasonography (US) of the liver was performed in 176 patients with confirmed diagnosis of cancer of the stomach and colon. All the nodules detected were either resected or needle biopsied for histological diagnosis. The results of the liver US were compared with those of pre-operative trans-abdominal US, CT scanning and intraoperative exploration. RESULTS Liver metastasis was detected by intraoperative US in 43 of the 176 patients (24.4%), with a total of 81 nodules found. Liver metastasis was confirmed histologically in 42 of the 43 cases (97.7%), the frequency of which was significantly higher than that of preoperative transabdominal US, CT scan and surgical exploration (P < 0.05, P < 0.01). It was particularly superior for the detection of liver metastasis less than 2 cm in diameter. CONCLUSION Intraoperative ultrasonography is sensitive enough to early detect tumors of the stomach and colon metastasized to the liver.
Collapse
Affiliation(s)
- L Lin
- Union Hospital of Fujian Medical University, Fujian Provincial Ultrasonic Medicine Institute, Fuzhou 350001, China
| | | | | |
Collapse
|