917 search results for “bioactive molecules” in the Public website
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DNA expressions - A formal notation for DNA
Promotores: J.N. Kok, H.J. Hoogeboom
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Development of highly accurate density functionals for H2 dissociation on transition metals
Metals surfaces form a group of effective catalysts for the reaction of small molecules such as hydrogen (H2).
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Modern Drug Discovery
How are new drugs developed? This question is central to the Minor Modern Drug Discovery (MDD), which covers the entire trajectory from disease to drug molecule and vice versa. The various research groups involved offer a complementary and interdisciplinary perspective by connecting the diverse subjects…
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Finding and valorizing new antibiotics using AI
Antibiotics are a class of medicine most people take for granted. But pathogenic bacteria are becoming more and more resistant to our antibiotics, and this poses a great challenge for future treatments. There is thus a great societal need to identify new molecules that can address new targets and be…
- Jan van Ruitenbeek Lab - Atomic and Molecular Conductors
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Frontiers in surface scattering simulations
Theorists have recently made substantial progress in simulating reactive molecule-metal surface scattering but still face major challenges. The grand challenge is to develop an approach that enables accurate predictive calculations of reactions involving electronically excited states with potential…
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Electroextraction approaches for preconcentration of metabolites
In this thesis, we developed new ways to use a technique called electroextraction (EE) to extract charged molecules from one liquid into another using an electric field.
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Quantitative Super-Resolution Microscopy
Promotor: T. Schmidt
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Laura Heitman
Science
l.h.heitman@lacdr.leidenuniv.nl | +31 71 527 4558
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Marcel Schaaf
Science
m.j.m.schaaf@biology.leidenuniv.nl | +31 71 527 4975
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Unlocking the chemistry of the heavens
How are the building blocks of life formed?
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Using AI to improve the Design-Make-Test cycle with Galapagos
Researchers at LED3 are working together with biopharmaceutical company Galapagos to develop software for use in early drug discovery (funded by NWO). This software is able to design molecules with several simultaneously optimized characteristics and will also take prediction reliability into consideration…
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More effective blocking of CCR2 receptor
The discovery of new medicines is a tedious and lengthy process. On average, over 10,000 molecules need to be studied for one to become a drug and reach the patient. Part of that process are the very costly clinical trials in humans, and candidate drugs often fail due to side effects or lack of efficacy.…
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Understanding membrane fusion at the molecular level using a biomimetic model system
How can the transport of molecules in living cells help to target medicines at exactly the right place?
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Phylogenetic ecology of octocoral - gastropod associations
Promotor: E. Gittenberger, Co-promotores: L.P. van Ofwegen; B.W. Hoeksema
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Innovative strategies to clinically characterize the human tear proteome
Transplantation of labial salivary glands to the eyelids for patients with dry eye appears to give excellent results clinically.
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Rapid and profound rewiring of brain lipid signaling networks by acute diacylglycerol lipase inhibition
Diacylglycerol lipases (DAGLα and DAGLβ) convert diacylglycerol to the endocannabinoid 2-arachidonoylglycerol. Our understanding of DAGL function has been hindered by a lack of chemical probes that can perturb these enzymes in vivo.
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Key publications
Key publications of the Computational Drug Discovery group
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Michel Orrit receives Spinoza Prize in Royal Theatre
On September 12, Michel Orrit received his Spinoza prize in the Royal Theatre in The Hague from OCW Secretary of State Sander Dekker. With the award comes a budget of 2.5 million euro, to be spent freely on scientific research, and the coveted Spinoza statue. Orrit shared the honor with Eveline Crone…
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Michel Orrit wins Physica Prize 2016
Michel Orrit was awarded the Physica prize 2016 for his groundbreaking work on single molecule spectroscopy.
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Physicist Michel Orrit new member KNAW
The Royal Netherlands Academy of Arts and Sciences (KNAW) selects prominent researchers as members based on their scientific achievements. On September 17th, the KNAW will install 21 new members, including Leiden physicist Michel Orrit.
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Michel Orrit and Hermen Overkleeft members KNAW
The Royal Netherlands Academy of Arts and Sciences (KNAW) selects prominent researchers as members based on their scientific achievements. On September 17th, the KNAW will install 21 new members, including Leiden physicist Michel Orrit and chemist Hermen Overkleeft.
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Uncovering the ingredients for planet formation
This thesis discusses the physical and chemical processes than influence the composition of forming planets.
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PhD Theses
A full overview of THEOR PhD theses.
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Chemistry between stars and planets
In the large gas clouds between the stars, chemical reactions take place under extreme conditions, giving rise to both small molecules, such as water and common salt, as well as large complex molecules that can serve as the building blocks of life. This is known as astrochemistry and it is something…
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Affinity-based profiling of the adenosine receptors
The adenosine receptors are proteins that reside in the extracellular membranes of cells. Activation of adenosine receptors plays a role in many physiological and pathological processes, such as immune responses and cancers.
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New generation of graphene biosensors based on smooth surfaces and sharp edges
The surface and the edges of graphene are expected to provide higher sensitivity and specificity in detecting and characterizing single molecules. However fundamental physical limits exist in reaching an ultimate precision in detecting the dynamics of chemical and biological systems. The research in…
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Elucidating the catalytic properties of gold
How does CO adsorption on gold promote its own oxidation and the oxidation of other organic molecules?
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Reactivity on interstellar ice analogues
The
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To explore the drug space smarter: Artificial intelligence in drug design for G protein-coupled receptors
Over several decades, a variety of computational methods for drug discovery have been proposed and applied in practice. With the accumulation of data and the development of machine learning methods, computational drug design methods have gradually shifted to a new paradigm, i.e. deep learning methods…
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Research
Research at the THEOR group is comprised of the following research themes:
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Research
Developing computational algorithms for structural biology -A high resolution, three dimensional view of a molecule provides detailed information that help elucidate its function: by knowing the exact arrangement of atoms in a molecule, we can understand disease, develop drugs to combat them and improve…
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Laboratory studies of Water Ice in Space
Astronomical observations of cold regions in the universe show a rich inventory of ices. Part of these ices may end up on planets like our own, but in that journey they will be exposed to considerable amounts of radiation.
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Data mining and algorithm development
Due to the modern techniques of combinatorial chemistry and high-throughput screening, data on the biological activity of many millions of compounds is known. However, it is still very difficult to transfer this data into knowledge: if we know that compounds A and B bind to a certain protein with high…
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NWO grants two IBL-proposals by interdisciplinary research consortia
Recently, NWO has decided to grant two interdisciplinary research proposals for national and international consortia submitted by researchers from the Institute of Biology Leiden. One of the proposals is led by Prof. dr. Ariane Briegel, the other one by dr. Remko Offringa.
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Physics and Engineering Approaches to Biomedicine and Pharmacology
Mashaghi lab conducts research at the interface of physics, engineering and biomedicine. We develop and use theoretical and experimental approaches to address basic and applied research problems.
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Research lines
Physics and Engineering Approaches to Biomedicine and Pharmacology
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Gas-surface reaction dynamics and surface science
The local ordering of atoms at the surface of a metallic particle determines its catalytic activity and selectivity. As energy systems of the future will be based on efficient catalytic conversion of small molecules in closed cycles, we study how structural effects of catalysts can be used to our ad…
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Novel target engagement biomarkers for better drug candidates
Is is possible to better predict the validity of drug candidates?
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Novel chemical tools for target validation in neuroinflammation
In what way can new tools and techniques be used to develop drug candidates for the treatment of neurological disorders?
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Non-equilibrium chemistry and cooling in simulations of galaxy formation
Promotor: J. Schaye
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Highly Efficient Activation of HCl Dissociation on Au(111) via Rotational Preexcitation
The probability for dissociation of molecules on metal surfaces, which often controls the rate of industrially important catalytic processes, can depend strongly on how energy is partitioned in the incident molecule. There are many example systems where the addition of vibrational energy promotes reaction…
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A new method to reconstruct the structure from crystal images
Promotor: J.P. Abrahams, Co-promotor: T. Grüne
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1,2-cis-glycosylations: method development and synthesis of complex oligosaccharides
Promotor: G.A. van der Marel, Co-promotor: D.C. Codée
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Fatema Zahra Rashid
Science
f.z.m.rashid@lic.leidenuniv.nl | +31 71 527 1037
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Amin Moradi
Science
moradi@physics.leidenuniv.nl | +31 71 527 5676
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Hortus botanicus
Hidden behind the Academy Building on the Rapenburg lies the oldest botanical garden of the Netherlands and one of the oldest gardens in the world. Founded in 1590 and expanded in the following centuries, the Hortus is the green heart of Leiden.
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Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation
Source: PLoS ONE, Volume 10, Issue 3 (2015)
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Dynamic hydrogels as synthetic extracellular matrices for three- dimensional cell culture
Synthetic hydrogels that mimic the natural extracellular matrix in the biophysical and biochemical cues it provides to cells are in high demand, however the cell phenotypes as they are observed in vivo in numerous cases have yet to be attained.
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Chemical Probe Facility
The Chemical Probe Facility is part of the Leiden Early Drug Discovery & Development (LED3) center. Activity-based protein profiling (ABPP) is one of the pillars of chemical biology. ABPP determines the activity of entire protein families in living cells and tissues under physiological conditions, such…