DL COMP BIOTECH

 % Define the PDB ID you want to download pdb_id = 'desired PDB ID'; % Replace with your desired PDB ID ,    % Construct the URL for the PDB file pdb_url = strcat('https://files.rcsb.org/download/', pdb_id, '.pdb'); % Specify the download location on your computer download_dir = 'path_to_save_directory'; % Replace with your desired download directory % Create the full path for the downloaded file download_path = fullfile(download_dir, strcat(pdb_id, '.pdb')); % Download the PDB file try     pdb_data = webread(pdb_url);          % Open the file in binary write mode     fid = fopen(download_path, 'wb');          % Write the PDB data as binary     fwrite(fid, pdb_data);          % Close the file     fclose(fid);          disp(['PDB file ', pdb_id, ' downloaded successfully to ', download_path]); catch     error(' Failed to ...

A momentous revelation unfolded in the distant echoes of 1552 B.C., casting a light on the enigma that would later be named diabetes. Hesy-Ra, an Egyptian physician and an astute observer of the human condition, etched history's first known account of diabetes symptoms. In the papyrus scrolls of time, he chronicled frequent urination as a symptom of a mysterious disease that also caused emaciation. Intriguingly, the ancients of that age also witnessed a curious phenomenon. They noted with fascination that the ants were drawn to the very essence of this enigmatic ailment – the urine of those afflicted by it. Thus, the symphony of nature's elements was orchestrating an age-old ballet, and ants were the first humble spectators drawn to a substance that held secrets beyond their ken.  Centuries drifted by, and like the vigilant ants drawn to secrets held in the urine, a new cast of spectators took the stage. These unique individuals, dubbed "water tasters," embarked on an...

Let's go back to our days of algebra and consider there was a person named X.  X was 82 years older and was suffering from an aggressive form of blood cancer. He already had to go through six courses of chemotherapy, but the wait to be cured was still a far cry. His saviors, the doctors, whom, in his poem, D. H. Lawrence has ornamented as “ the ones who work with science and arts, and knows the secrets of the mill”, were systematically evaluating a roster of conventional cancer medications. Their aim was to discover an effective solution, methodically eliminating options one by one." Needless to say, the drugs were doing everything but cure X. The hopes were dying, and they were taking X with them, slowly, on a bed adorned with the persistent presence of suffering. But then the doctors, knowing that there was nothing to lose, decided to embrace a boon that, until then, had remained just an elusive dream, hovering ever closer to the realm of reality: the boon of Artificial inte...

P ancreatic malignancies exhibit a multifaceted microenvironment, governing metabolic shifts and fostering a dynamic interplay among diverse cell populations residing in this specialised area. Despite the decade-long endeavours to predominantly elucidate the most lethal pancreatic malignancy, Pancreatic ductal adenocarcinoma (PDAC) continues to stand as one of the most lethal forms of cancer. Adding more concerns, it has been hypothesised that PDAC will overtake colorectal cancer before 2040, moving only behind lung cancer as a leading cause of cancer-related mortality. With almost 97% of oncology trials failing to reach the clinical stage, the dreadful question arises, “Was a solution ever there?”. Cut back through the decades, a hope amidst all odds can be seen, where the culprit cells driving the spread of pancreatic cancer have been identified. Maybe it could be premature enthusiasm to say that we have now found the weakness to target, but a hope is always a hope, and we can be che...

Proteins constitute the primary foundation of life, serving as pivotal components in the execution of vital life functions. Therefore, the essential task of functionally annotating proteins is paramount for comprehending life processes at the molecular level. For this purpose, various computational methods based on machine learning and deep learning, such as biological sequence analysis, protein structure prediction, and medical image processing, have been published. Typically, machine learning methods amalgamate features extracted from diverse data sources to assess the similarity between proteins and functional terms, leading to the annotation of similar functions for proteins exhibiting this likeness. Models based on deep learning typically emphasize extracting protein sequence features using convolutional neural networks and recurrent neural networks. They subsequently incorporate sequence similarity, protein-protein interaction (PPI) network data, and other information to enhance ...

 In the ever-expanding realm of scientific research, staying updated with the latest developments and understanding the interconnectedness of various studies is a formidable challenge. This is where "Connected Papers" steps in as a valuable tool for researchers and academics. This blog will delve into the functionalities and usefulness of Connected Papers in the world of scientific exploration. The Power of Visualizing Connections Connected Papers isn't just another academic search engine; it's a bridge between the isolated islands of scientific knowledge. It harnesses the power of visualization to present academic papers in an interconnected web, allowing researchers to see at a glance how different studies relate to one another. By simply entering the title of a paper, users are presented with a network of related research. This visualization provides a holistic view of a particular field of study, making it easier to spot trends and gaps in the research landscape. ...

QSAR (Quantitative Structure-Activity Relationship) and pharmacophore modeling are two different computational techniques used in drug discovery, but they have different focuses and applications. QSAR is a technique that uses mathematical and statistical models to predict the biological activity or properties of a compound based on its chemical structure and related properties. QSAR models are generated using a set of molecular descriptors, which are numerical representations of a molecule's chemical and physical properties. QSAR models are useful for predicting the activity of compounds and for identifying potential drug candidates. Pharmacophore modeling, on the other hand, is a technique that focuses on identifying the essential structural and chemical features of a ligand (a molecule that binds to a receptor) that are responsible for its biological activity. The goal of pharmacophore modeling is to generate a three-dimensional (3D) representation of the essential features of a ...

Reaction coordinates or collective variables are quantities that are used to describe the progression of a reaction or a process of interest in a biomolecular system. Reaction coordinates or collective variables can be either geometric or dynamic, and are defined based on the specific system being studied. Geometric reaction coordinates are based on the spatial arrangement of the atoms or molecules in the system, such as the distance between two atoms, the angle between two bonds, or the dihedral angle between four atoms. Dynamic reaction coordinates, on the other hand, describe the motion or behavior of the system over time, such as the root mean square deviation (RMSD) of a protein structure, the radius of gyration, or the number of hydrogen bonds formed. By tracking reaction coordinates or collective variables, advanced MD simulations can help to identify the most probable reaction pathways, transition states, and free energy landscapes for a given process. For example, a ligand bin...

 Steered molecular dynamics (SMD) simulation is a type of molecular dynamics simulation that is used to study the response of a biomolecule to an applied force or an external perturbation. In SMD simulations, a force is applied to a subset of atoms within the biomolecule, typically using an external potential, to simulate the effect of a physical process such as protein unfolding, ligand binding or transport of ions across a membrane. The force is applied in a controlled and gradual manner, allowing the biomolecule to respond to the force and explore different conformational states. During an SMD simulation, the forces acting on the subset of atoms are continuously updated to maintain a specific pulling speed or force constant. The resulting changes in the structure and dynamics of the biomolecule can be analyzed to provide insights into its function and behavior under different conditions. SMD simulations can be used to study a wide range of biological processes, such as protein-l...

A general protocol for ligand docking using Glide: Preparation of receptor and ligand structures: The receptor structure should be prepared by adding missing atoms, assigning charges, and optimizing the geometry. The ligand structure should be prepared by generating multiple conformations and assigning charges. Generation of the receptor grid: Glide generates a grid that represents the receptor binding site. The grid is generated by defining the dimensions of the binding site, assigning van der Waals and electrostatic interaction potentials to the grid points, and scaling and translating the receptor structure to fit the grid. Ligand docking: Glide docks the ligand onto the receptor grid by generating and evaluating different ligand conformations and orientations. Glide uses a Monte Carlo algorithm to sample the conformational space and evaluate the fitness of each pose based on a scoring function. Post-docking analysis: After docking, Glide generates a list of ligand poses ranked by t...

India has made significant contributions to science and technology over the years, but it has lagged behind in Nobel Prize recognition. Some of the reasons for this could include: Lack of resources and funding : As mentioned earlier, India has limited resources and funding available for research. This can make it challenging for Indian scientists and researchers to carry out groundbreaking research, which is often a requirement for Nobel Prize recognition. Brain Drain : As talented scientists and researchers leave India to pursue better opportunities abroad, it can lead to a talent shortage in the country. This can hinder progress in research and development, and impact the chances of Indian scientists winning Nobel Prizes. Inadequate recognition and reward systems : The current reward system in India does not always value and recognize contributions to science and technology. This can discourage scientists and researchers from pursuing cutting-edge research, and make it less likely fo...

 OPLS (Optimized Potentials for Liquid Simulations) and AMBER (Assisted Model Building with Energy Refinement) force fields are widely used in molecular dynamics simulations. OPLS3 and OPLS4 are the third and fourth versions of the OPLS force field, respectively. The main difference between OPLS3 and OPLS4 is the addition of new dihedral angle parameters in OPLS4, which allow for a more accurate description of torsional profiles. OPLS4 also includes improved electrostatic parameters, including an updated partial charge model and more accurate Lennard-Jones parameters. AMBER 14SB and AMBER19SB are both versions of the AMBER force field. The main difference between AMBER 14SB and AMBER19SB is the incorporation of updated protein backbone and side-chain torsional parameters, which were derived from quantum mechanics calculations. AMBER19SB also includes updated electrostatic parameters, including the use of the AM1-BCC partial charge model. Overall, OPLS4 and AMBER19SB are more recent...