Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

详细信息    查看全文

• 作者：Pedro Sfriso ; Agusti Emperador ; Laura Orellana ; Adam Hospital ; Josep Lluis Gelp铆 ; Modesto Orozco
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2012
• 出版时间：November 13, 2012
• 年：2012
• 卷：8
• 期：11
• 页码：4707-4718
• 全文大小：784K
• 年卷期：v.8,no.11(November 13, 2012)
• ISSN：1549-9626

文摘

We present a new method for estimating pathways for conformational transitions in macromolecules from the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell鈥揇emon sampling techniques. The method can work with high efficiency at different levels of resolution, including the atomistic one, and can help to define initial pathways for further exploration by means of more accurate atomistic molecular dynamics simulations. The method is implemented in a freely available Web-based application accessible at mmb.irbbarcelona.org/MDdMD" class="extLink">http://mmb.irbbarcelona.org/MDdMD.