CSA Trust Grant: Recent Awardees

2024

Ariadna Peiro, is currently a PhD student in the Cheminformatics and Nutrition Research Group at Rivira i Virgill University, Spain. Her thesis focuses on the fields of virtual screening and drug discovery, with an emphasis on SARS-CoV-2 Proteases. She is involved in a project called NEXT-PANDEMICS that was created after the coronavirus pandemic in response to the vast amount of data generated from vaccine and antiviral research. The main objective of the project is to develop new open-source tools to enhance the effectiveness of virtual screening and predict binding affinity in silico. Additionally, these tools will be applied to determine a list of leads to search for antivirals. Moreover, this discovery would be applied to Zika and Dengue viruses.  CSA Trust Grant funds will be used to attend summer courses at the Strasbourg summer school in Cheminformatics.

Nils van Staalduinen is a PhD candidate at the Institute for Physical Chemistry, RWTH Aachen Germany where he works under the guidance of Prof. Bannwarth, focusing on theoretical chemistry and cheminformatics. His research concentrates on MolBar, a molecular identifier for chemical structure databases. His current work is an extension of his Master’s thesis for which he won the MSE Master Award of RWTH Aachen. MolBar was launched in March 2024 and has since been downloaded several hundred times. He balances his PhD work with a role at BASF SE, where he further develops chemical database pipelines with a focus on cheminformatics algorithms that streamline molecule registration and tautomer searchers.

His CSA Trust grant funds will provide financial support for research visits to the laboratory of Professor Todd Martinez (see: Martinez Lab Group page) for the integration of MolBar into the Nanoreactor at Stanford University (CA) and for payment of travel expenses to attend two conferences – the 2024 German Cheminformatics Conference and the 2024 RDKit UGM.

Ivan Yankov is currently a PhD student at the University of Strathclyde (U.K). His research is focused on integrating Artificial Intelligence (AI)  methods into computational design across drug discovery, drug development, and structure determination of biological materials. The goal is to accelerate in-silico design pipelines by modelling thermodynamic properties of nucleic acids and their complexes. Furthermore, AI NMR data analysis systems can be fine-tuned to nucleic acid and nucleic acid ligand complexes to eliminate inefficiencies and reproducibility challenges in the structure determination process from NMR data. The innovation will eliminate bottle necks in the in-silico design and structure determination stages.

2023

David Dalmau Ginesta, who received a Master’s degree in 2021 from the University of Zaragoza (Spain). He was awarded a highly competitive “pre-doctoral grant” from the Aragon Government to pursue his PhD studies in the same laboratory. He incorporated Dr. Juan V. Alegre Requena as a new supervisor to improve his skills in computational chemistry and programming and started developing cheminformatics and machine learning tools applicable to various sectors of computational chemistry (Note: Dr. Alegre Requena was a 2022 recipient of the CSA Trust Grant for the purpose of establishing his own research group). Ginesta is requesting funds to attend two international conferences (the RSEQ XXXIX Biennial Meeting in Zaragoza (Spain), June 25-29, 2023, and the ACS fall in San Francisco (USA), August 13-17, 2023. He will be presenting papers at both conferences on the ROBERT  program that his research group has recently developed. This is a free and open-source Python package aiming to provide high-level ML protocols accessible to all users via GitHub. The software includes five modules: curate, generate, testing, predict and AQME-ROBERT, offering complete and diverse ML workflows. Input options include CSV and JSON databases with descriptors, as well as SMILES inputs via the AQME-ROBERT tandem. ROBERT is easy to install and can be used via command lines, Jupyter Notebooks, and SLURM scripts. Overall, ROBERT provides users with a comprehensive, transparent, and reproducible ML workflow to generate highly accurate predictions with minimal user intervention. This program has potential in multiple chemistry fields, including drug discovery, materials science, chemical synthesis, and catalyst discovery.

Heidi Klem will be receiving her PhD from Colorado State University (USA) in June 2023 and was selected to be a National Research Council postdoctoral associate at the U.S. National Institute of Standards and Technology (NIST) as of August 2023 as a result of her research proposal. She was awarded funds to spend a month visiting Professor Zhongyue John Yang at Vanderbilt University, Nashville, TN (USA) for one month. Prof. Yang is the SC Family Dean’s Faculty Fellow and an Assistant Professor of Chemistry, Chemical Engineering, and Data Science. He is a prominent investigator in the field of data-driven and high-throughput enzyme modeling with notable contributions such as EnzyHTP,1 and IntEnzyDB.2 EnzyHTP is a state-of-the-art Python software that automates model generation, QM, MM and multiscale (i.e., QM/MM) simulations, and data analysis. During her visit she will be immersed in Prof. Yang’s research group to gain direct training in the software development and application of EnzyHTP and IntEnzyDB. These training experiences will contribute significantly to the success of her NIST research proposal – the development of a standardized protocol for the generation and validation of quantum mechanical QM-based enzyme models. The results of this work will be incorporated into a model generation and validation workflow, available to the community as an open-source, Python-based package. As noted by the National Academies of Sciences, Engineering, and Medicine in a 2019 consensus report, Reproducibility and Replicability in Science, computational workflows are exceedingly valuable to facilitate reproducibility. This workflow can be used in the development of NIST Standard Reference Data (SRD) in the form of pre-validated enzyme models to expedite biocatalysis investigations, validate new methods on previously benchmarked systems and promote data-driven characterization of enzyme scaffold design principles.

Dr. Md Bin Yeamin, received his PhD in computational and experimental chemistry in 2021 from the University Rovira I Virgili, Spain. He is currently a postdoctoral fellow at the University of Girona, researching dual catalysis in alkyne functionalization and predictive catalysis in hydrogenation and CO2 fixation. With his expertise in structured Python and ML techniques, he intends to apply Machine Learning to mechanistic modeling for predicting reaction barriers and yields. He was awarded funds to support two activities. First, a month-long research stay in June 2023 at the Alegre group at ISQCH Institute of CSIC-Universidad de Zaragona to launch a collaborative project on predicting catalytic performances and reaction mechanisms from data-driven automated machine learning (ML) methods. Second, his abstract on gem-Hydrogenation leading to Enyne Cycloisomerization” has been accepted for an oral presentation at the XXXIX Biennial Meeting – Spanish Royal Society of Chemistry (RSEQ) 2023 under the symposium S15. Recent trends in organometallic Reactivity.

2022

Dr. Juan V. Alegra Requena was awarded $1,892 for travel to present his work at the RSEQ XXXVIII Biennial meeting in Granada, Spain in June, 2022 and the 8^th EuChemS Chemistry Congress in Lisbon, Portugal in September 2022. As of April 2022, he has a Juan de la Cierva contract at the University of Zaragoza, Spain where he is establishing his own research group focusing on computational mechanisms and Machine Learning. He is additionally developing cheminformatics tools for multiple purposes such as data manipulation, automated supporting information creation and Machine Learning modeling. One of the most important codes is GoodVibes, a useful tool used to gather, analyze, check, and present thermochemistry data from multiple quantum mechanical programs.

Dr. Beatrice Chiew was awarded $4,034 to present her work at the Royal Australian Chemistry Institute National Congress in July 2022 and the EFMC International symposium on medicinal chemistry in September. She is a a postdoc at the University of Newcastle, Australia, where she is   working on drug development in the space of Dynamin endocytosis inhibitors. Her PhD work was on the development of a novel fragment-to-lead workflow to expedite the development of chemical probes against the DNA damage protein 53BP1 for use against BRCA-1 breast cancer. She continues to explore these fragments through purchasable analogues using a novel cheminformatic algorithm called GRADe.

2021

Call for Grant proposals not circulated due to the pandemic.2020

2020

Daniel Csókás, a member of Professor Imre Pápai’s research team at the Research Centre for Natural Sciences, Budapest, Hungary, was awarded $,4000 to travel to the University of Bristol (UK) to expand the scope of his experience in computational chemistry and to acquire new skills and research techniques in the area of data-led catalyst design. The project will involve the creation of a ligand knowledge base for tridentate ligands using calculated descriptors. The database will then be processed to retrieve structural and reactivity information about tridentate ligands and their transition metal complexes. The award is pending the lifting of travel restrictions, due to the pandemic.

Andrew Tarzia, a research associate at the Imperial College London, was awarded $3,500 to visit Asst. Prof. Cory Simon at Oregon State University for three weeks in 2021 to initiate a collaboration in the use of machine learning algorithms to predict host-guest finding affinities based upon molecular shapes. The award is pending the lifting of travel restrictions, due to the pandemic.

Nicola Knight, an Enterprise Research Fellow in the Physical Sciences Data-Science Service (PSDS) at the University of Southampton (UK), works with the newly-established national research facility to provide access to chemistry and physical sciences data at a national scale and to increase not only the breadth of the data, but also the ways in which the data can be used by the scientific community. She was awarded $2,500 to fund efforts related to a knowledge-sharing retreat that will involve four early-career researchers (ECRs) from a cross section of research domains to participate in a 3-day workshop on the depiction of chemical information using the FAIR principles.

2019

Guilian Luchini, Colorado State University, Fort Collins, CO, was awarded funds to attend the Chemical Society Meeting that will be held August 24-29 in San Diego, CA to present his research in applying often-overlooked corrections to DFT frequency calculations in an automated fashion.

Roi Rutenberg, Chemistry Department at Stanford University, Stanford, CA, was awarded funds for travel to visit the University of Illinois, Chicago in order to model molecular dynamic (MD) simulations at the Kral group as part of his research related to retrieving information about pEtN cellulose’s chemical structure as an individual compound, as well as a partner in future chemical reactions.

Monika Szabo, Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia, was awarded funds for travel to attend two conferences at which she will present her research on drugs for myelofibrosis. The conferences are: EFMC-ASMC’19 International Symposium on Advances in Synthetic and Medicinal Chemistry – Athens Greece; 1st-5th September 2019, and the 20th SCI/RSC Medicinal Chemistry Symposium-Cambridge UK; 8th-11th September, 2019.

2018

Stephen Capuzzi, Division of Chemical Biology and Medicinal Chemistry at the University of North Carolina Chapel Hill Eshelman School of Pharmacy, U.S.A., was awarded a grant to attend the 31s ICAR in Porto, Portugal from 06/11/2018 to 06/15/2018, where he presented his research entitled “Computer-Aided Discovery and Characterization of Novel Ebola Virus Inhibitors.”

Christopher Cooper, Cavendish Laboratory, University of Cambridge, U.K, was awarded a grant to present his current research on systematic, high-throughput screening of organic dyes for co- sensitized dye-sensitized solar cells. He presented his work at the Solar Energy Conversion Gordon Research Conference and Seminar held June 16-22, 2018 in Hong Kong.

Mark Driver, Chemistry Department, University of Cambridge, U.K., was awarded a grant to offset costs to attend the 7th EUCheMS conference where he will present a poster on his research that focuses on the development and applications of a theoretical approach to model hydrogen bonding.

Genqing Wang, La Trobe Institute for Molecular Sciences, La Trobe University, Australia, was awarded a grant to present his work at the Fragment-Based Lead Discovery Conference (FBLD2018) in San Diego, USA in October 2018. The current focus of his work is the development of novel anti-virulence drugs which potentially overcome the problems of antibiotic resistance of Gram-negative bacteria.

Roshan Singh, University of Oxford, U.K., was awarded a grant to conduct research within Dr. Marcus Lundberg’s Group at Uppsala University, Sweden, as part of a collaboration that he has set up between them and Professor Edward Solomon’s Group at Stanford University, California. He conducts research within Professor John McGrady’s group at the University of Oxford. The collaboration will look to consolidate the experiments on heme Fe (IV)=O complexes currently being studied by Solomon’s Group with future multireference calculations to be conducted within Lundberg’s Group.

2017

Jesus Calvo-Castro, University of Hertfordshire, England, was awarded a Grant to cover travel to present his workd at the Fifth International Conference on Novel Psychoactive Substances to be held in Vienna, Austria from August 23-23, 2017. He works on the development of novel methodologies for the in-the-field detection of novel psychoactive substances (NPS), where chemical structure and information play a crucial role.

Jessica Holien, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia,was awarded a Grant to cover travel to present her work at the 2017 Computer-Aided Drug Design (CADD) Gordon Research Conference scheduled to take place July 16-21, 2017 in Mount Snow, VT, USA. She is a Postdoctoral researcher at St. Vincent’s and is responsible for a range of computational molecular modelling including; compound database development, virtual screening, docking, homology modelling, dynamic simulations, and drug design.

2016

Thomas Coudrat, Monash University, Australia, was awarded a Grant to cover travel to present his work at three meetings in the United States: the Open Eye Scientific CUP XVI, The American Chemical Society Spring Meeting, and the Molsoft ICM User Group Meeting. His work is in ligand directed modeling.

Clarisse Pean, Chimie Paris Tech, France, was awarded a Grant to cover travel to give an invited presentation at the 2016 Pacific Rim Meeting on Electrochemical and Solid State Science later this year.

Qian Peng, University of Oxford, England, was awarded a Grant to attend the 23rd IUPAC Conference on Physical Organic Chemistry. His research is in the development of new ligands for asymmetric catalysis.

Petteri Vainikka, University of Turku, Finland, was awarded a Grant to spend the summer developing and testing new methods for modelling organic solvents in organic solutions with Dr. David Palmer and his group at the University of Strathclyde, Glasgow, Scotland.

Qi Zhang, Fudan University, China, was awarded a Grant to attend a Gordon Conference on Enzymes, coenzymes and metabolic pathways. His research is in enzymatic reactions.

2015

Dr. Marta Encisco,  Molecular Modeling Group, Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Australia was awarded a Grant to cover travel costs to visit collaborators at universities in Spain and Germany and to present her work at the European Biophysical Societies Association Conference in Dresden, Germany in July 2015.

Jack Evans, School of Physical Science, University of Adelaide, Australia was awarded a grant to spend two weeks collaborating with the research group of Dr. Francois-Xavaier Coudert (CNRS, Chimie Paris Tech).

Dr. Oxelandr Isayer, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmaacy, University of North Carolina at Chapel Hill, was awarded a Grant to attend summer classes at the Deep Learning Summer School 2015 (University of Montreal) to expand his knowledge of machine learning to include Deep Learning (DL). His goal is to apply DL to chemical systems to improve predictive models of chemical bioactivity.

Aleix Gimeno Vives, Cheminformatics and Nutrition Research Group, Biochemistry and Biotechnology Dept., Universitat Rovira I Virgili, Spain, was awarded a Grant to attend the Cresset European User Group Meeting in June 2015 in order to improve his knowledge of the software that he is using to determine what makes an inhibitor selective for PTP1B.

2014

Dr. Adam Madarasz, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences. He was awarded a Grant for travel to study at the University of Oxford with Dr. Robert S. Paton, a 2013 CSA Trust Grant winner, in order to increase his experience in the development of computational methodology which is able to accurately model realistic and flexible transition states in chemical and biochemical reactions.

Maria José Ojeda Montes, Department of Biochemistry and Biotechnology, University Rovira i Virgili, Spain. She was awarded a Grant for travel expenses to study for four months at the Freie University of Berlin to enhance her experience and knowledge regarding virtual screening workflows for predicting therapeutic uses of Natural molecules in the field if functional food design.

Dr. David Palmer, Department of Chemistry, University of Strathclyde, Scotland.  He was awarded a Grant to present a paper at the fall 2014 meeting of the American Chemical Society on a new approach to representing molecular structures in computers based upon on ideas from the Integral Equation Theory of Molecular Liquids.

Sona B. Warrier,  Departments of Pharmaceutical Chemistry, Pharmaceutical Biotechnology, and Pharmaceutical Analysis, NMIMS University, Mumbai. She was awarded a Grant to attend the International Conference on Pure and Applied Chemistry to present a poster on her research on inverse virtual screening in drug repositioning.

2013

Dr. Johannes Hachmann, Department of Chemistry and Chemical Biology at Harvard University, Cambridge, MA.   He was awarded the Grant for travel to speak on “Structure-property relationships of molecular precursors to organic electronics at a workshop sponsored by the Centre Européen de Calcul Atomique et Moléculaire (CECAM) that will take place October 22 – 25, 2013 in Lausanne, Switzerland. .

Dr. Robert S. Paton, University of Oxford, UK.  He was awarded the Grant to speak at the Sixth Asian Pacific Conference of Theoretical and Computational Chemistry in Korea on July 11, 2013. Receiving the invitation for this meeting has provided Dr. Paton with an opportunity to further his career as a Principal Investigator.

Dr. Aaron Thornton, Material Science and Engineering at CSIRO in Victoria, Australia. He was awarded the Grant to attend the 2014 International Conference on Molecular and Materials Informatics at Iowa State University with the objective of expanding his knowledge of web semantics, chemical mark-up language, resource description frameworks and other on-line sharing tools.  He will also visit Dr. Maciej Haranczyk, a prior CSA Trust Grant recipient, who is one of the world leaders in virtual screening.

2012

Tu C. Le, CSIRO Division of Materials Science & Engineering, Clayton, VIV, Australia. She was awarded the Grant for travel to attend a Cheminformatics course at Sheffield University and to visit the Membrane Biophysics group of the Department of Chemistry at imperial College London.

2011

B. Brown, Kyoto University, Kyoto, Japan. J.B. was awarded the Grant for travel to work with Professor Ernst Walter-Knappat the Freie University of Berlin and Professor Jean-Phillipe Vert of the Paris MinesTech to continue his work on the development of atomic partial charge kernels

2010

Noel O’Boyle,  University College Cork, Ireland. Noel was awarded the grant to both network and present his work on open source software for pharmacophore discovery and searching at the 2010 German Conference on Cheminformatics.

2009

Laura Guasch Pamies, University Rovira & Virgili, Catalonia, Spain.  Laura was awarded the Grant to do three months of research at the University of Innsbruck, Austria.

2008

Maciej Haranczyk,  University of Gdansk, Poland. Maciej was awarded the Grant to travel to Sheffield University, Sheffield, UK, for a 6-week visit for research purposes.

2007

Rajarshi Guha,  Indiana University, Bloomington, IN, USA. Rajarshi was awarded the Grant to attend the Gordon Research Conference on Computer Aided Design in August 2007.

2006

Krisztina Boda, University of Erlangen, Erlangen, Germany.    Krisztina was awarded the Grant to attend the 2006 spring National Meeting of the American Chemical Society in Atlanta, GA, USA.

2005

Dr. Val Gillet and Professor Peter Willett, University of Sheffield, Sheffield, UK.  They were awarded the Grant for student travel costs to the 2005 Chemical Structures Conference held in Noordwijkerhout, the Netherlands.

2004

Dr. Sandra Saunders, University of Western Australia, Perth, Australia. Sandra was awarded the Grant to purchase equipment needed for her research.

2003

Prashant S. Kharkar, Institute of Chemical Technology, University of Mumbai, Matunga, Mumbai. Prashant was awarded the Grant to attend the conference, Bioactive Discovery in the New Millennium, in, Lorne, Victoria, Australia (February 2003) to present a paper, The Docking Analysis of 5-Deazapteridine Inhibitors of Mycobacterium avium complex (MAC) Dihydrofolate reductase (DHFR).

2001

Georgios Gkoutos, Imperial College of Science, Technology and Medicine, Dept. of Chemistry. London, UK. Georgios was awarded the Grant to attend the conference, Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, (CMTPI-2001) in Bordeaux, France, to present part of his work on internet-based molecular resource discovery tools.