<< Chapter < Page Chapter >> Page >
The CHARMM all-atom empirical potential function

For more information on CHARMM and the CHARMM force field, please see The CHARMM website.

Applications of roadmap methods

Kinetics of protein folding

The two standard methods of simulating protein motion are molecular dynamics simulation (MD) and Monte Carlo simulation (MC). In MD, a molecule or system of molecules is given an initial set of atomic momenta, placed in a potential field, and allowed to evolve over time following Newton's equations of motion and the forces exerted on it by the field. In MC, a series of perturbations is applied to a single molecule. After each perturbation, if the estimated energy of the molecule has decreased, the perturbed conformation is used for the next step of the simulation. If the energy has increased, the perturbed conformation might be accepted, with a probability that drops off sharply as the energy change increases. Otherwise, the perturbed conformation is rejected and the previous conformation is perturbed again. Properly implemented MC or MD simulations, run for long enough, should generate a series of conformations with a Boltzmann-like distribution of structures (see the first section of this module for a reminder of what the Boltzmann distribution looks like).

The problem with these methods is that they are very slow. A single MD simulation of a few nanoseconds of motion for an average-size protein, performed on a cluster of processors, can take days, and such simulations are of limited reliability due to approximations of energy and to the extremely short time periods that can be simulated in a reasonable amount of CPU time. Simulations must be repeated to determine what a reasonable, average behavior might look like. Some protein rearrangement events take place on a scale of microseconds, milliseconds, or even seconds, so a trajectory of a few nanoseconds cannot hope to capture these low-frequency events.

The field of chemical kinetics is concerned with the rate at which chemical processes take place, and therefore, the pathways and mechanisms by which they occur. In protein biochemistry, one of the major open questions is the protein folding problem: Given a protein, and its folded (native) and unfolded (denatured) structures, what is the mechanism by which the protein folds into its native state? Currently (2006), it is possible to determine in the laboratory the rate at which a protein folds and sometimes the form of its transition state, the highest energy conformation(s) it assumes in the process of folding. These laboratory measurements can be compared to those inferred from simulation, and the quality of the simulation can thereby be indirectly estimated.

Roadmap-based algorithms to study this problem began with work by Latombe, Singh, and Brutlag in 1999 , in which they attempted to use a PRM to find and study protein binding pockets. This work led directly to that of Song and Amato, Apaydin and Latombe, and Singal and Pande, all presented below. Existing methods as of early 2006 are presented.

Questions & Answers

what does preconceived mean
sammie Reply
physiological Psychology
Nwosu Reply
How can I develope my cognitive domain
Amanyire Reply
why is communication effective
Dakolo Reply
Communication is effective because it allows individuals to share ideas, thoughts, and information with others.
effective communication can lead to improved outcomes in various settings, including personal relationships, business environments, and educational settings. By communicating effectively, individuals can negotiate effectively, solve problems collaboratively, and work towards common goals.
it starts up serve and return practice/assessments.it helps find voice talking therapy also assessments through relaxed conversation.
miss
Every time someone flushes a toilet in the apartment building, the person begins to jumb back automatically after hearing the flush, before the water temperature changes. Identify the types of learning, if it is classical conditioning identify the NS, UCS, CS and CR. If it is operant conditioning, identify the type of consequence positive reinforcement, negative reinforcement or punishment
Wekolamo Reply
please i need answer
Wekolamo
because it helps many people around the world to understand how to interact with other people and understand them well, for example at work (job).
Manix Reply
Agreed 👍 There are many parts of our brains and behaviors, we really need to get to know. Blessings for everyone and happy Sunday!
ARC
A child is a member of community not society elucidate ?
JESSY Reply
Isn't practices worldwide, be it psychology, be it science. isn't much just a false belief of control over something the mind cannot truly comprehend?
Simon Reply
compare and contrast skinner's perspective on personality development on freud
namakula Reply
Skinner skipped the whole unconscious phenomenon and rather emphasized on classical conditioning
war
explain how nature and nurture affect the development and later the productivity of an individual.
Amesalu Reply
nature is an hereditary factor while nurture is an environmental factor which constitute an individual personality. so if an individual's parent has a deviant behavior and was also brought up in an deviant environment, observation of the behavior and the inborn trait we make the individual deviant.
Samuel
I am taking this course because I am hoping that I could somehow learn more about my chosen field of interest and due to the fact that being a PsyD really ignites my passion as an individual the more I hope to learn about developing and literally explore the complexity of my critical thinking skills
Zyryn Reply
good👍
Jonathan
and having a good philosophy of the world is like a sandwich and a peanut butter 👍
Jonathan
generally amnesi how long yrs memory loss
Kelu Reply
interpersonal relationships
Abdulfatai Reply
What would be the best educational aid(s) for gifted kids/savants?
Heidi Reply
treat them normal, if they want help then give them. that will make everyone happy
Saurabh
What are the treatment for autism?
Magret Reply
hello. autism is a umbrella term. autistic kids have different disorder overlapping. for example. a kid may show symptoms of ADHD and also learning disabilities. before treatment please make sure the kid doesn't have physical disabilities like hearing..vision..speech problem. sometimes these
Jharna
continue.. sometimes due to these physical problems..the diagnosis may be misdiagnosed. treatment for autism. well it depends on the severity. since autistic kids have problems in communicating and adopting to the environment.. it's best to expose the child in situations where the child
Jharna
child interact with other kids under doc supervision. play therapy. speech therapy. Engaging in different activities that activate most parts of the brain.. like drawing..painting. matching color board game. string and beads game. the more you interact with the child the more effective
Jharna
results you'll get.. please consult a therapist to know what suits best on your child. and last as a parent. I know sometimes it's overwhelming to guide a special kid. but trust the process and be strong and patient as a parent.
Jharna
Got questions? Join the online conversation and get instant answers!
Jobilize.com Reply

Get Jobilize Job Search Mobile App in your pocket Now!

Get it on Google Play Download on the App Store Now




Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'Geometric methods in structural computational biology' conversation and receive update notifications?

Ask