Search for dissertations about: "Protein-ligand binding interactions"

Showing result 1 - 5 of 26 swedish dissertations containing the words Protein-ligand binding interactions.

2. 1. Theoretical studies of protein-ligand binding

   Author : Majda Misini Ignjatovic; Beräkningskemi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Protein-ligand binding; MD; GIST; GCMC; FEP; Solvation; Entropy; Water; QM MM-FEP; Protein-ligand binding; MD; GIST; GCMC; FEP; Solvation; Entropy; Water; QM MM-FEP;

   Abstract : Understanding how drugs work is of great importance, since it can facilitate drug discovery, both time- and costwise. At the same time, it is important to have methods that can help predict how well does a potential drug molecule bind to its target. Computational methods can in many ways contribute to drug design process. READ MORE

4. 2. Theoretical Studies of Protein-Ligand Interactions

   Author : Kuang Guanglin; Tu Yaoquan; Bulone Vincent; David van der Spoel; KTH; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Binding free energy; molecular dynamics; molecular docking; metadynamics; nicotinic receptor; amyloid fibril; PH domain; Theoretical Chemistry and Biology; Teoretisk kemi och biologi;

   Abstract : The protein-ligand interaction is an important issue in rational drug design and protein function research. This thesis focuses on the study of protein-ligand interactions using various molecular modeling methods, which are used in combination to predict the binding modes and calculate the binding free energies of several important protein-ligand systems, as summarized below. READ MORE

5. 3. Multivariate design of molecular docking experiments : An investigation of protein-ligand interactions

   Author : David Andersson; Anna Linusson Jonsson; Gabriele Cruciani; Umeå universitet; []
   Keywords : MEDICIN OCH HÄLSOVETENSKAP; MEDICAL AND HEALTH SCIENCES; Molecular docking; chemometrics; multivariate analysis; principal component analysis; PCA; design of experiments; DoE; partial least-square projections to latent structures; PLS; scoring functions; ligand-binding cavity; major histocompatibility complex; MHC; glycopeptide; T-cell.; Pharmaceutical chemistry; Läkemedelskemi; datorlingvistik; computational linguistics;

   Abstract : To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. READ MORE

6. 4. Computational Studies of Protein-ligand Systems Using Enhanced Sampling Methods

   Author : Rongfeng Zou; Yaoquan Tu; Leif Eriksson; KTH; []
   Keywords : molecular dynamics; enhanced sampling; protein-ligand interactions; umbrella sampling; metadynamics; Teoretisk kemi och biologi; Theoretical Chemistry and Biology;

   Abstract : This thesis focuses on studies of protein-ligand systems using enhanced sampling methods. In chapter I, I give a brief introduction to the time-scale problem and some enhanced sampling methods. In chapter II, the basics of MD simulation are reviewed. READ MORE

7. 5. Modeling Kinetics of Protein-Ligand Systems

   Author : Yang Zhou; Yaoquan Tu; Hans Ågren; David van der Spoel; KTH; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; Teoretisk kemi och biologi; Theoretical Chemistry and Biology;

   Abstract : Protein-ligand interactions dominate many life activities and are crucial for thedevelopment of tracers for diagnosing diseases and drugs for treating diseases.For protein-ligand interactions, the binding affinity is conventionally believedto be the most important indicator. READ MORE