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Cincilla G, Masoni S, Blobel J. Individual and collective human intelligence in drug design: evaluating the search strategy. J Cheminform 2021; 13:80. [PMID: 34635158 PMCID: PMC8507178 DOI: 10.1186/s13321-021-00556-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/18/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, individual and collective human intelligence, defined as the knowledge, skills, reasoning and intuition of individuals and groups, have been used in combination with computer algorithms to solve complex scientific problems. Such approach was successfully used in different research fields such as: structural biology, comparative genomics, macromolecular crystallography and RNA design. Herein we describe an attempt to use a similar approach in small-molecule drug discovery, specifically to drive search strategies of de novo drug design. This is assessed with a case study that consists of a series of public experiments in which participants had to explore the huge chemical space in silico to find predefined compounds by designing molecules and analyzing the score associate with them. Such a process may be seen as an instantaneous surrogate of the classical design-make-test cycles carried out by medicinal chemists during the drug discovery hit to lead phase but not hindered by long synthesis and testing times. We present first findings on (1) assessing human intelligence in chemical space exploration, (2) comparing individual and collective human intelligence performance in this task and (3) contrasting some human and artificial intelligence achievements in de novo drug design.
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Affiliation(s)
- Giovanni Cincilla
- Molomics, Barcelona Science Park, c/Baldiri i Reixac 4-12, 08028, Barcelona, Spain.
| | - Simone Masoni
- Molomics, Barcelona Science Park, c/Baldiri i Reixac 4-12, 08028, Barcelona, Spain.
| | - Jascha Blobel
- Molomics, Barcelona Science Park, c/Baldiri i Reixac 4-12, 08028, Barcelona, Spain.
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2
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Das R, Keep B, Washington P, Riedel-Kruse IH. Scientific Discovery Games for Biomedical Research. Annu Rev Biomed Data Sci 2019; 2:253-279. [PMID: 34308269 DOI: 10.1146/annurev-biodatasci-072018-021139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Over the past decade, scientific discovery games (SDGs) have emerged as a viable approach for biomedical research, engaging hundreds of thousands of volunteer players and resulting in numerous scientific publications. After describing the origins of this novel research approach, we review the scientific output of SDGs across molecular modeling, sequence alignment, neuroscience, pathology, cellular biology, genomics, and human cognition. We find compelling results and technical innovations arising in problem-oriented games such as Foldit and Eterna and in data-oriented games such as EyeWire and Project Discovery. We discuss emergent properties of player communities shared across different projects, including the diversity of communities and the extraordinary contributions of some volunteers, such as paper writing. Finally, we highlight connections to artificial intelligence, biological cloud laboratories, new game genres, science education, and open science that may drive the next generation of SDGs.
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Affiliation(s)
- Rhiju Das
- Department of Biochemistry and Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Keep
- Department of Learning Sciences, Stanford University, Stanford, California 94305, USA
| | - Peter Washington
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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Hu X, Duan J, Dang D. Crowdsourcing-based semantic relation recognition for natural language questions over RDF data. ENTERP INF SYST-UK 2019. [DOI: 10.1080/17517575.2019.1597385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Xin Hu
- College of Information Science and Technology, Beijing Normal University, Beijing, China
| | - Jiangli Duan
- Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Depeng Dang
- College of Information Science and Technology, Beijing Normal University, Beijing, China
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4
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Mura C, Draizen EJ, Bourne PE. Structural biology meets data science: does anything change? Curr Opin Struct Biol 2018; 52:95-102. [PMID: 30267935 DOI: 10.1016/j.sbi.2018.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/31/2018] [Accepted: 09/07/2018] [Indexed: 01/22/2023]
Abstract
Data science has emerged from the proliferation of digital data, coupled with advances in algorithms, software and hardware (e.g., GPU computing). Innovations in structural biology have been driven by similar factors, spurring us to ask: can these two fields impact one another in deep and hitherto unforeseen ways? We posit that the answer is yes. New biological knowledge lies in the relationships between sequence, structure, function and disease, all of which play out on the stage of evolution, and data science enables us to elucidate these relationships at scale. Here, we consider the above question from the five key pillars of data science: acquisition, engineering, analytics, visualization and policy, with an emphasis on machine learning as the premier analytics approach.
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Affiliation(s)
- Cameron Mura
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Eli J Draizen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Philip E Bourne
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Data Science Institute, University of Virginia, Charlottesville, VA 22904, USA.
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Jorda J, Sawaya MR, Yeates TO. Progress in low-resolution ab initio phasing with CrowdPhase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:446-53. [PMID: 26960132 PMCID: PMC4784676 DOI: 10.1107/s2059798316003405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 02/26/2016] [Indexed: 11/21/2022]
Abstract
New developments in CrowdPhase, a collaborative online game for tackling the low-resolution phase problem, are presented. The new features address several crystallographic issues and extend the reach of CrowdPhase to a broader range of experimental data sets. Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.
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Affiliation(s)
- Julien Jorda
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
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Lunin VY, Lunina NL, Petrova TE, Baumstark MW, Urzhumtsev AG. Mask-based approach to phasing of single-particle diffraction data. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:147-57. [DOI: 10.1107/s2059798315022652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/25/2015] [Indexed: 11/10/2022]
Abstract
A Monte Carlo-type approach for low- and medium-resolution phasing of single-particle diffraction data is suggested. Firstly, the single-particle phase problem is substituted with the phase problem for an imaginary crystal. A unit cell of this crystal contains a single isolated particle surrounded by a large volume of bulk solvent. The developed phasing procedure then generates a large number of connected and finite molecular masks, calculates their Fourier coefficients, selects the sets with magnitudes that are highly correlated with the experimental values and finally aligns the selected phase sets and calculates the averaged phase values. A test with the known structure of monomeric photosystem II resulted in phases that have 97% correlation with the exact phases in the full 25 Å resolution shell (1054 structure factors) and correlations of 99, 94, 81 and 79% for the resolution shells ∞–60, 60–40, 40–30 and 30–25 Å, respectively. The same procedure may be used for crystallographicab initiophasing.
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Bentzien J, Bharadwaj R, Thompson DC. Crowdsourcing in pharma: a strategic framework. Drug Discov Today 2015; 20:874-83. [PMID: 25637169 DOI: 10.1016/j.drudis.2015.01.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/24/2014] [Accepted: 01/19/2015] [Indexed: 11/16/2022]
Abstract
Conceptually, all organizations can be described as coordinated actors working together to deliver a product(s), or provide a service(s). For organizations to remain competitive, it is important to have processes that look outward for external 'innovations' that could improve how work is done, and what is delivered. We present a comprehensive review of a variety of processes that pharmaceutical companies have used to engage external actors ('the crowd') to provide innovation in the service of delivering novel therapeutic agents. This culminates in a framework that provides a consolidated view of crowdsourcing processes, which in turn enables a strategic application of a crowdsourcing methodology based on problem type.
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Affiliation(s)
- Jörg Bentzien
- Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Ragu Bharadwaj
- Appirio, 760 Market St, 11th Floor, San Francisco, CA 94102, USA
| | - David C Thompson
- Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA.
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