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In this comprehensive video, I cover basics of motifs, transcription factors, regulatory regions (promoters, enhancers, silencers, insulators), how motifs are represented and questions that Transcription Factor Binding Site (TFBS) analysis can help to answer. Furthermore, I list down various available tools to perform motif discovery and motif ...

This video tutorial accompanies Chapter 12 of 'Genetics: Genes, Genomes, and Evolution' by Meneely, Hoang, Okeke, and Heston. https://global.oup.com/academic/product/genetics-9780198712558 © Oxford University Press

Regulatory evolution by transcription-factor duplication Prof. Naama Barkai Dept. of Molecular Genetics, Weizmann Institute of Science Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge was studied in a few cases only. To provide ...

https://www.ibiology.org/cell-biology/cohesin The cohesin protein complex joins sister chromatids together before they are segregated during mitosis. In this talk, Dr. Peters presents evidence that cohesin also plays an important role in DNA folding and genome organization. Talk Overview: It has been known for many years that the protein ...

In this video, we show you how to locate transcription factor binding sites using GeneQuest.

Transcription Factor Binding Sites (TFBSs) Transcription factors are proteins with DNA binding activity that are involved in the regulation of transcription. Generally, TFs modulate gene expression by binding to gene promoter regions or to distal regions called enhancers. The distance between a TFBS and a transcription start site (TSS) of a ...

Transcription factor binding site prediction in vivo using DNA sequence and shape features - Anthony Mathelier - RECOMB/RSG 2015

Match is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses a library of positional weight matrices from TRANSFAC® Public 6.0. http://gene-regulation.com/

This webinar gives an introduction to the information required to effectively interpret ligand binding sites in protein structures. It will highlight tools available at the Protein Data Bank in Europe (PDBe) and PDBe Knowledge Base (PDBe-KB) to analyse ligand binding pockets and interactions. It will also highlight how this information can be ...

The crossbridge cycle describes the calcium-dependent interaction of actin and myosin during muscle contraction. Intracellular calcium binds troponin and causes a conformational change, leading to the movement of tropomyosin out of the myosin-binding site on actin. The myosin head binds actin at a 90° angle, forming a crossbridge. Further ...

https://www.ibiology.org/cell-biology/cohesin The cohesin protein complex joins sister chromatids together before they are segregated during mitosis. In this talk, Dr. Peters presents evidence that cohesin also plays an important role in DNA folding and genome organization. Talk Overview: It has been known for many years that the protein ...

Transcription factors control which genes are expressed and when. Part of the A Level Biology course. Specifically this relates to AQA Biology A Level Section 3.8

Schrodinger-PCI webinar Thirteenth Day 06-10-2020 Demonstration-3 (Binding site identification/Site map analysis) of the online webinar series on “Introduction to Computational Drug Design” Jointly organized by Pharmacy Council of India in coordination with Schrodinger. Various academic and industry partners such as Manipal Academy of ...

In this comprehensive video, we perform motif discovery and find enriched transcription factor binding sites (TFBS) using TRANSFAC in genomic regions of interest i.e ChIP-Seq peaks. geneXplain's point and click interface requires no programming to run the workflows and generate meaningful insights from high throughput data. In this ...

#cysticfibrosis Cystic fibrosis | CFTR gene mutation | Molecular mechanism | Bio science Cystic fibrosis (CF) is an inherited disorder that causes severe damage to the lungs, digestive system and other organs in the body. Cystic fibrosis affects the cells that produce mucus, sweat and digestive juices. These secreted fluids are normally thin ...

Link to Google Colab: https://colab.research.google.com/github/ash100 Welcome to Bioinformatics Insights. This video will make you able to use your receptor protein and calculate ligand-binding sites before docking setup. We will use Google Colab setup, and I will train you to use the structures directly from the PDB, or to use Uniprot ...

Jennifer E. Phillips-Cremins, Ph.D. is a tenured associate professor and Deans’ Faculty Fellow in Engineering and Medicine in the Departments of Genetics and Bioengineering at the University of Pennsylvania. During her Ph.D. candidacy at Georgia Institute of Technology, Dr. Cremins was funded by an NSF Graduate Research Fellowship to develop ...

Brief introduction to epigenetic regulation including the the two states of chromatin: euchromatin and heterochromatin. Transcript Epigenetic regulation encompasses a number of different modifications to chromatin. These include methylation of the DNA on cytosine bases, a modification that can further be oxidized, as well as modification of the ...

Illumina sequencing is a next generation sequencing method used to sequence millions of DNA fragments in parallel. In this video, we're going to explain how Illumina sequencing works. Standard Illumina sequencing can be split into the following steps: 1. Fragmentation 2. Addition of primer binding sites and capture sequences 3. Denaturation 4 ...

References/Resources: https://www.patreon.com/the_Crux The first major step in the cycle of eukaryotic transcription - INITIATION! We talk about the assembly of general transcription factors (GTFs) associated with RNA polymerase II and look at the role of each GTF in the mechanistic production of a pre-initiation complex (PIC). The PIC ...

Discussion of TADs and A/B compartments, as well as how to identify them from heatmap visualizations. MCB 182: Introduction to Genomics lecture videos Course playlist: https://www.youtube.com/playlist?list=PLpzXFzEHUCQdveBWm63MbUdGK_t0Nt23F

Abstract A fundamental challenge in studying cell function and disease is understanding how cis-regulatory regions control gene expression. Sequences of these regions specify the binding sites of multiple transcription factors, and understanding regulatory function requires the understanding of how multiple transcription factors bind ...

Portal is the home of the AI for drug discovery community. Join for more details on this talk and to connect with the speakers: https://portal.valencelabs.com/logg Protein-protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design ...

(USMLE topics) Molecular basis of the sliding filament theory (skeletal muscle contraction) - the cross bridge cycle. Purchase a license to download a non-watermarked copy of this video on AlilaMedicalMedia(dot)com Voice by: Sue Stern ©Alila Medical Media. All rights reserved. Muscle contraction is at the basis of all skeletal movements ...

Receptor tyrosine kinases (RTKs) are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Of the 90 unique tyrosine kinase genes identified in the human genome, 59 encode receptor tyrosine kinase proteins. Most RTKs are single subunit receptors but some exist as multimeric complexes, e.g., the ...

Some Notes to go with the video (recommended to read after the video) Protein sorting between the nucleus and the cytosol is termed gated transport, with the gate being the nuclear pore complex, or NPC. The nucleus has a double membrane surrounding it called the nuclear envelope. The nucleus allows passive entry and exit of small molecules ...

https://explorebiology.org/videos/enhancer A short sequence of DNA (50-1500 base pairs) that is recognized by specific proteins, generally known as activators, that act to help increase the chance that its associated gene will be transcribed.

This video describes several DNA binding motifs present in wide variety of Transcription factors and also describes how they interact with DNA with proper examples

This is a video tutorial version of the article found here https://bioinformaticsreview.com/20161214/how-to-perform-docking-in-a-specific-binding-site-using-autodock-vina/

What takes place at the neuromuscular junction!? Are you curious about how your brain tells your muscles to move? Dive into the fascinating world of the neuromuscular junction (NMJ)—the critical connection between nerves and muscles that powers every movement in your body! 🧠💪 In this video, we'll break down: 🔹 The anatomy of the NMJ ...

In this video, I have explained my understanding on What is a Binding Site ? What is an Active Site ? What is Protein-Ligand Docking ? What is a Ligand ? Also I have demonstrated how to vizualise the Binding site present on a protein, using PyMOL Tool (Academic Version / Educaitonal License). This video is intended for teaching purpose.

Show your love by hitting that SUBSCRIBE button! :) Translation Part 3 - Elongation & Ribosome Sites

The tutorial will guide you through the step-by-step procedure to dock a small molecule ligand amino acid (L-Asp) to a protein receptor (AspRS) by using AutoDock Vina integrated with Chimera. Model system: Aspartyl-tRNA-synthetase.

Circular Dichroism Spectroscopy is a useful technique for characterization of secondary structure of proteins. Additionally, it can be used to monitor protein structural stability, cofactor binding sites in proteins, and to study protein folding. I discuss the theory and applications of CD Spectroscopy in this video.

Show your love by hitting that SUBSCRIBE button! :) Enzymes 4 - Enzyme-Substrate Binding

This video provides a tutorial on initiation process of translation. There are three distinct phases of mRNA translation, 1) initiation, 2) elongation and 3) termination. Key components required for translation initiation are, 1) mRNA, 2) ribosomal subunits, 3) initiator tRNA, 4) initiation protein factors and 4) GTP to generate energy. Small ...

Researchers have identified more than 1,700 mutations in the cystic fibrosis gene. Different CF mutations are grouped into classes or types, based on the way the mutations affect the key protein (called CFTR) produced by the CF gene. Using these classes of mutations can help scientists and doctors better understand CF and develop new potential ...

This webinar is produced by MolSoft LLC www.molsoft.com for more information please contact info@molsoft.com 8:55 How to run the pocket finding tool 16:00 How to change the display of the pockets, surface, coloring, lighting etc.. 20:00 How to display the residues making contact with the pocket 26:50 Pocket properties - DLID score (from Merck ...

Understanding the precise binding sites of antibodies on their target antigens can significantly advance the discovery and development of new therapeutics and vaccines, providing critical insights into mechanisms of action and protection. While there are numerous approaches for epitope mapping, comprehensive, high-throughput mutagenesis has ...

Discovery Studio is a comprehensive software suite for analyzing and modeling molecular structures, sequences, and other data of relevance to life science researchers. In this tutorial and other related tutorials we will be looking at how to use Discovery studio for proteomics. You can download and Install Discovery studio from the following ...

This video animation shows how gene editing might one day be used to edit mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that cause cystic fibrosis. This is one potential option for a cure to CF. Learn more about gene editing in CF: https://www.cff.org/Research/Research-Into-the-Disease/Restore-CFTR-Function ...

Link to protnix server: http://101.126.11.40:8000/ Welcome to Bioinformatics Insights. This video demonstration will teach you the usage of AlphaFold3 or protenix (a reproduction of AlphaFold3) to model biological systems with all kinds of ligands. You will also learn that how we can perform docking with AlphaFold3. #google #deepmind # ...

Ho describes different approaches for therapeutic antibody discovery. He then introduces the concept of antibody binding site as therapeutics and takes a deep dive into the utility of single-chain variable fragment (scFv) and single domain antibodies in therapeutics.

How protein binding can affect the distribution of the drug in the body? Drugs can bind to plasma proteins which is a reversible process whereas they can also bind to tissue proteins resulting in long term interaction. #plasmaprotein #liphophilicity #tissueprotein

The objective of this experiment is to identify and analyze binding sites within a protein structure. These sites are critical for understanding interactions with ligands, substrates, or other macromolecules, essential for protein function. Binding sites on proteins are specific regions where ligands or other molecules interact. This ...

Are you still relying on outdated or incomplete transcription factor databases? In this video, we explore why TRANSFAC® is not just a nice-to-have — it's an essential resource for any lab working in genomics, transcriptomics, or molecular biology. 🔍 Learn how TRANSFAC helps you: Identify transcription factor binding sites with unmatched ...

CTCF binding prediction using genomic and epigenomic features - Camilo Villaman - SCS - Poster - ISMB 2022