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Stochastic roadmap simulation for the study of ligand-protein interactions

M. S. Apaydin, C. E. Guestrin, C. Varma, D. L. Brutlag, J.-C. Latombe
2002 Bioinformatics  
In this paper, we establish the use of Stochastic Roadmap Simulation (SRS) for the study of ligand-protein interactions through two studies.  ...  In our application of SRS to the domain of ligand-protein interactions, we consider a new parameter called escape time, the expected number of MC simulation steps required for the ligand to escape from  ...  Singh for his ligand-protein modeling code.  ... 
doi:10.1093/bioinformatics/18.suppl_2.s18 pmid:12385979 fatcat:vztq5amzijbutfdrqq7pu7uhjm

Stochastic Conformational Roadmaps for Computing Ensemble Properties of Molecular Motion [chapter]

Mehmet Serkan Apaydın, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe
2004 Springer Tracts in Advanced Robotics  
A salient feature of this new approach is that it examines all the paths in the roadmap simultaneously, rather than one at a time as classic methods such as Monte Carlo (MC) simulation would do.  ...  ., properties characterizing the average behavior of many pathways. We construct a directed graph, called stochastic conformational roadmap, whose nodes are randomly sampled molecule conformations.  ...  Snoeyink for helpful discussions. We also thank C. Varma for preparing the energy files for some of the ligand-protein complexes.  ... 
doi:10.1007/978-3-540-45058-0_9 fatcat:q4nkvg5lgvczrcgpz7g3tqztya

Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion

Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe, Chris Varma
2003 Journal of Computational Biology  
Computational studies on ligand-protein binding also demonstrate SRS as a promising approach to study ligand-protein interactions.  ...  This paper introduces Stochastic Roadmap Simulation (SRS) as a new computational approach for exploring the kinetics of molecular motion by simultaneously examining multiple pathways.  ...  Guestrin was supported by a Siebel Scholarship and by the Sloan Foundation. We thank D. Koller, V. Pande and J. Snoeyink for helpful discussions, A. Singh for the ligand-protein modelling software.  ... 
doi:10.1089/10665270360688011 pmid:12935328 fatcat:pd7tieovcfhdvmpavaw2swagoe

Stochastic roadmap simulation

Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe
2002 Proceedings of the sixth annual international conference on Computational biology - RECOMB '02  
We introduce Stochastic Roadmap Simulation (SRS), a new approach for exploring the kinetics of molecular motion by simultaneously examining multiple pathways encoded compactly in a graph, called a roadmap  ...  To test the effectiveness of our approach, we apply it to the computation of the transmission coefficients for protein folding, an important order parameter that measures the "kinetic distance" of a protein's  ...  Apaydin was supported by the D.L. Cheriton Stanford Graduate Fellowship. Brutlag was supported National Human Genome Research Institute grant HGF02235.  ... 
doi:10.1145/565196.565199 dblp:conf/recomb/ApaydinBGHL02 fatcat:hib6yzafzjg2jdncn7eljpbkba

Motion planning algorithms for molecular simulations: A survey

Ibrahim Al-Bluwi, Thierry Siméon, Juan Cortés
2012 Computer Science Review  
From the point of view of applications, the survey deals with problems involving protein folding and conformational transitions, as well as protein-ligand interactions.  ...  This paper concerns the latter domain, providing a survey on motion planning algorithms applied to molecular modeling and simulation.  ...  Acknowledgments This work has been partially supported by the French National Agency for Research (ANR) under project GlucoDesign.  ... 
doi:10.1016/j.cosrev.2012.07.002 fatcat:ipdgrtcxqrczvoyi5vi7bpnlzy

Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation [chapter]

Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe
2006 Lecture Notes in Computer Science  
It uses the recently introduced Stochastic Roadmap Simulation (SRS) method to estimate the transition state ensemble (TSE) and predict the rates and Φ-values for protein folding.  ...  This paper presents a new method for studying protein folding kinetics.  ...  Hsu's research is partially supported by grant R252-000-145-112 from the National University of Singapore. J.C.  ... 
doi:10.1007/11732990_34 fatcat:uunypasdnbh4fbpnpkkdgmgxni

Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values

Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe
2007 Journal of Computational Biology  
It uses the recently introduced Stochastic Roadmap Simulation (SRS) method to estimate the transition state ensemble (TSE) and predict the rates and the Φ-values for protein folding.  ...  This paper presents a new method for studying protein folding kinetics.  ...  Latombe's research is partially supported by NSF grant DMS-0443939, and part of this work was completed, while was a visiting professor at the National University of Singapore, supported by the Kwan Im  ... 
doi:10.1089/cmb.2007.r004 pmid:17683262 fatcat:tws4zbwfmrgetnmev3idh76r5y

Roadmap Methods for Protein Folding [chapter]

Mark Moll, David Schwarz, Lydia E. Kavraki
2008 Protein Structure Prediction  
Protein folding refers to the process whereby a protein assumes its intricate three-dimensional shape. is chapter reviews a class of methods for studying the folding process called roadmap methods.  ...  e goal of these methods is not to predict the folded structure of a protein, but rather to analyze the folding kinetics. It is assumed that the folded state is known.  ...  the  algorithm to study the docking of a ligand to a protein.  ... 
doi:10.1007/978-1-59745-574-9_9 pmid:18075168 fatcat:x5j72w7puzchvlmqge3vwuc3ce

The European Conference on Computational Biology 2002

Clare Sansom
2003 Comparative and Functional Genomics  
Analysis of the interaction between ligands and protein binding sites is an important part of many drug discovery programs, yet it is still difficult to detect the optimum position for ligand binding.  ...  The technique of stochastic roadmap simulation (SRS; not to be confused with the Sequence Retrieval System that is familiar to most bioinformaticians) maps a complex conformational problem in three-dimensional  ... 
doi:10.1002/cfg.256 pmid:18629090 pmcid:PMC2447376 fatcat:zsoidjxl5raztmbdpllcwjr5nq

Towards Understanding the Messengers of Extracellular Space: Computational Models of Outside-In Integrin Reaction Networks

Zeynep Karagöz, Laura Rijns, Patricia Y.W. Dankers, Martijn van Griensven, Aurélie Carlier
2020 Computational and Structural Biotechnology Journal  
The interactions between cells and their extracellular matrix (ECM) are critically important for homeostatic control of cell growth, proliferation, differentiation and apoptosis.  ...  However, the versatility in molecular pathways integrins are involved in, the high diversity in their interaction partners both outside and inside the cell as well as on the cell membrane and the short  ...  AC kindly acknowledges the Dutch province of Limburg in the LINK (FCL67723) (''Limburg INvesteert in haar Kenniseconomie") knowledge economy project.  ... 
doi:10.1016/j.csbj.2020.12.025 pmid:33425258 pmcid:PMC7779863 fatcat:57spdhbnxfchzdcrb43l2qlnkq

Computational Models of Protein Kinematics and Dynamics: Beyond Simulation

Bryant Gipson, David Hsu, Lydia E. Kavraki, Jean-Claude Latombe
2012 Annual Review of Analytical Chemistry  
For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger domain-level picture of protein dynamics can be revealed.  ...  Such simulations can be prohibitively difficult or lengthy, however, for large proteins or in probing the lower resolution, long-timescale behaviors of proteins generally.  ...  Physics-based simulations (1-3) offer a direct method to study proteins by describing physical interactions among atoms and numerically solving the associated equations of motion.  ... 
doi:10.1146/annurev-anchem-062011-143024 pmid:22524225 pmcid:PMC4866812 fatcat:t4btthioyrdt7hu3tpbnwum3kq

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu, Bert L. de Groot
2016 PLoS Computational Biology  
Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics  ...  This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of  ...  The review in [23] summarizes many studies that observe conformational selection for protein-ligand, protein-protein, protein-DNA, protein-RNA and RNA-ligand interactions.  ... 
doi:10.1371/journal.pcbi.1004619 pmid:27124275 pmcid:PMC4849799 fatcat:gys3apbbbbb4tjr42k7yi3twpy

Modeling for (physical) biologists: an introduction to the rule-based approach

Lily A Chylek, Leonard A Harris, James R Faeder, William S Hlavacek
2015 Physical Biology  
Models that capture the chemical kinetics of cellular regulatory networks can be specified in terms of rules for biomolecular interactions.  ...  , which may be local, such as the state of a particular site or domain of a protein.  ...  Acknowledgments This work was supported by grants R25GM105608, P50GM085273, and P41GM103712 from the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) and  ... 
doi:10.1088/1478-3975/12/4/045007 pmid:26178138 pmcid:PMC4526164 fatcat:fddxndhab5cazbhziyxxvtan24

Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning

Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao
2020 Frontiers in Molecular Biosciences  
and discovery of allosteric modulators for therapeutically important protein targets.  ...  The wealth of structural and functional information along with diversity and complexity of allosteric mechanisms in therapeutically important protein families have provided a well-suited platform for development  ...  ACKNOWLEDGMENTS The authors acknowledge the technical assistance of Schmid College Grand Challenge Initiative Postdoctoral Fellow Dr. Anne Sonnenschein.  ... 
doi:10.3389/fmolb.2020.00136 pmid:32733918 pmcid:PMC7363947 fatcat:vxoqxun6ebhdveqlbwi7l7rfui

Computational Studies for Structure-Based Drug Designing Against Transmembrane Receptors: pLGICs and Class A GPCRs

Pavan V. Payghan, Indrani Bera, Dhananjay Bhattacharyya, Nanda Ghoshal
2018 Frontiers in Physics  
Addressing the multidimensional problem of understanding the structure and dynamics of such big proteins, multisite-protein-ligand complexes is now possible with molecular dynamics simulation approach,  ...  The advancement of computational science guided IMPs study even in the absence of crystal structures through the homology/comparative modeling approaches.  ...  All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication. ACKNOWLEDGMENTS  ... 
doi:10.3389/fphy.2018.00052 fatcat:fuu4aqb6avbcpp6n26yb5qkaxm
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