The cloud and other new computational methods to improve molecular modelling

Introduction: Industrial, as well as academic, drug discovery efforts are usually supported by computational modelling techniques. Many of these techniques, such as virtual high-throughput docking, pharmacophore-based screening of conformer databases and molecular dynamics simulations, are computationally very demanding. Depending on the parallelisation strategy applicable to the respective method, recent technologies based on central processing units, for example, cloud and grid computing, or graphics processing units (GPUs), can be employed to accelerate their execution times considerably. This allows the molecular modeller to look at larger data sets, or to use more accurate methods. Areas covered: The article introduces the recent developments in grid, cloud and GPU computing. The authors provide an overview of molecular modelling applications running on the above-mentioned hardware platforms and highlight caveats of the respective architectures, both from a theoretical and a practical point of view. Expert opinion: The architectures described can improve the molecular modelling process considerably, if the appropriate technologies are selected for the respective application. Despite these improvements, each of the individual computational platforms suffers from specific issues, which will need to be addressed in the future. Furthermore, current endeavours have focused on improving the performance of existing algorithms, rather than the development of new methods that explicitly harness these new technologies.

[1]  Jonathan D Hirst,et al.  Molecular Dynamics Simulations Using Graphics Processing Units , 2011, Molecular informatics.

[2]  Ji-Bo Wang,et al.  Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs , 2011, J. Chem. Inf. Model..

[3]  Santosh A. Khedkar,et al.  Successful applications of computer aided drug discovery: moving drugs from concept to the clinic. , 2010, Current topics in medicinal chemistry.

[4]  Antony J. Williams,et al.  Cheminformatics workflows using mobile apps , 2013 .

[5]  Romain Dolbeau,et al.  One OpenCL to rule them all? , 2013, 2013 IEEE 6th International Workshop on Multi-/Many-core Computing Systems (MuCoCoS).

[6]  Garrett M Morris,et al.  The emerging role of cloud computing in molecular modelling. , 2013, Journal of molecular graphics & modelling.

[7]  Kai Wang,et al.  Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics , 2013, Journal of Computer-Aided Molecular Design.

[8]  J. Xu OpenCL – The Open Standard for Parallel Programming of Heterogeneous Systems , 2009 .

[9]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[10]  Ryan G. Coleman,et al.  ZINC: A Free Tool to Discover Chemistry for Biology , 2012, J. Chem. Inf. Model..

[11]  Marc Stamminger,et al.  Fast GPU‐based Adaptive Tessellation with CUDA , 2009, Comput. Graph. Forum.

[12]  Marta Mattoso,et al.  Discovering drug targets for neglected diseases using a pharmacophylogenomic cloud workflow , 2012, 2012 IEEE 8th International Conference on E-Science.

[13]  Martin Hofmann-Apitius,et al.  WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures , 2009, Malaria Journal.

[14]  Péter Kacsuk,et al.  Using a private desktop grid system for accelerating drug discovery , 2011, Future Gener. Comput. Syst..

[15]  Ji-Bo Wang,et al.  GPU Accelerated Support Vector Machines for Mining High-Throughput Screening Data , 2009, J. Chem. Inf. Model..

[16]  Sally R. Ellingson,et al.  High‐throughput virtual molecular docking with AutoDockCloud , 2014, Concurr. Comput. Pract. Exp..

[17]  Martin Hofmann-Apitius,et al.  In silico drug discovery approaches on grid computing infrastructures. , 2010, Current clinical pharmacology.

[18]  Stephen R. Johnson,et al.  Grid computing in large pharmaceutical molecular modeling. , 2008, Drug discovery today.

[19]  Qian Zhang,et al.  Accelerated Conformational Entropy Calculations Using Graphic Processing Units , 2013, J. Chem. Inf. Model..

[20]  Shan Chang,et al.  A Parallel Molecular Docking Approach Based on Graphic Processing Unit , 2010, 2010 4th International Conference on Bioinformatics and Biomedical Engineering.

[21]  Ruibo Wu,et al.  Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing , 2013, J. Chem. Inf. Model..

[22]  Li Guo,et al.  Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics. , 2013, Journal of molecular graphics & modelling.

[23]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[24]  Bin Shen,et al.  GridMol: a grid application for molecular modeling and visualization , 2008, J. Comput. Aided Mol. Des..

[25]  Jens Krüger,et al.  From the Desktop to the Grid: conversion of KNIME Workflows to gUSE , 2013, IWSG.

[26]  Thomas Stützle,et al.  Accelerating Molecular Docking Calculations Using Graphics Processing Units , 2011, J. Chem. Inf. Model..

[27]  Sriram Krishnamoorthy,et al.  GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems. , 2011, Journal of chemical theory and computation.

[28]  Chee Keong Kwoh,et al.  GPU Accelerated Molecular Docking with Parallel Genetic Algorithm , 2012, 2012 IEEE 18th International Conference on Parallel and Distributed Systems.

[29]  Karl A. Wilkinson,et al.  Acceleration of the GAMESS‐UK electronic structure package on graphical processing units , 2011, J. Comput. Chem..

[30]  Andrzej M. Goscinski,et al.  A VMD Plugin for NAMD Simulations on Amazon EC2 , 2012, ICCS.

[31]  Fu Kit Sheong,et al.  A fast parallel clustering algorithm for molecular simulation trajectories , 2013, J. Comput. Chem..

[32]  Bo Hong,et al.  Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing , 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

[33]  Jee-In Kim,et al.  A molecular docking system using CUDA , 2009, ICHIT '09.

[34]  R. Altman,et al.  Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways , 2013, Nature chemistry.

[35]  Heather J Kulik,et al.  Ab initio quantum chemistry for protein structures. , 2012, The journal of physical chemistry. B.

[36]  Charles Perkins,et al.  Hydra: A Self Regenerating High Performance Computing Grid for Drug Discovery , 2008, J. Chem. Inf. Model..

[37]  Yanli Wang,et al.  PubChem: Integrated Platform of Small Molecules and Biological Activities , 2008 .

[38]  Klaus Schulten,et al.  GPU-accelerated molecular modeling coming of age. , 2010, Journal of molecular graphics & modelling.

[39]  J. Andrew McCammon,et al.  Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units , 2013, Journal of chemical theory and computation.

[40]  Johan Montagnat,et al.  Grid-enabled Virtual Screening Against Malaria , 2006, Journal of Grid Computing.

[41]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[42]  Vijay S. Pande,et al.  OpenMM: A Hardware-Independent Framework for Molecular Simulations , 2010, Computing in Science & Engineering.

[43]  Jie Luo,et al.  Retrieval of Crystallographically-Derived Molecular Geometry Information , 2004, J. Chem. Inf. Model..

[44]  Asim Munawar,et al.  A Bayesian Optimization Algorithm for De Novo ligand design based docking running over GPU , 2010, IEEE Congress on Evolutionary Computation.

[45]  Andrea Clematis,et al.  Cloud Infrastructures for In Silico Drug Discovery: Economic and Practical Aspects , 2013, BioMed research international.

[46]  Martin C. Herbordt,et al.  Fast binding site mapping using GPUs and CUDA , 2010, 2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW).

[47]  Bo Hong,et al.  A GPU-Based Approach to Accelerate Computational Protein-DNA Docking , 2012, Computing in Science & Engineering.

[48]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[49]  R. Glen,et al.  Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.

[50]  G.E. Moore,et al.  Cramming More Components Onto Integrated Circuits , 1998, Proceedings of the IEEE.

[51]  Maurizio Vichi,et al.  Studies in Classification Data Analysis and knowledge Organization , 2011 .

[52]  Klaus Schulten,et al.  GPU-accelerated molecular visualization on petascale supercomputing platforms , 2013, UltraVis@SC.

[53]  Andrew A. Chien,et al.  The future of microprocessors , 2011, Commun. ACM.

[54]  Christine M Isborn,et al.  Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. , 2012, Journal of chemical theory and computation.

[55]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[56]  Konstantinos Krampis,et al.  Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community , 2012, BMC Bioinformatics.

[57]  Pradeep Dubey,et al.  Debunking the 100X GPU vs. CPU myth: an evaluation of throughput computing on CPU and GPU , 2010, ISCA.

[58]  Hong Liu,et al.  GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit , 2013, J. Comput. Chem..

[59]  László Kaján,et al.  Cloud Prediction of Protein Structure and Function with PredictProtein for Debian , 2013, BioMed research international.

[60]  Ying Zhang,et al.  A Hadoop-based Massive Molecular Data Storage Solution for Virtual Screening , 2012, 2012 Seventh ChinaGrid Annual Conference.

[61]  Li Guo,et al.  Pyrolysis of Liulin Coal Simulated by GPU-Based ReaxFF MD with Cheminformatics Analysis , 2014 .

[62]  Li Liu,et al.  Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit. , 2011, Journal of chemical theory and computation.

[63]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.

[64]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born , 2012, Journal of chemical theory and computation.

[65]  Ani Anciaux-Sedrakian,et al.  Accelerating VASP electronic structure calculations using graphic processing units , 2012, J. Comput. Chem..

[66]  Maxwell Hutchinson,et al.  VASP on a GPU: Application to exact-exchange calculations of the stability of elemental boron , 2012, Comput. Phys. Commun..

[67]  Jiří Vondrášek,et al.  Increasing Affinity of Interferon-γ Receptor 1 to Interferon-γ by Computer-Aided Design , 2013, BioMed research international.

[68]  Shuo Zhou,et al.  CovalentDock Cloud: a web server for automated covalent docking , 2013, Nucleic Acids Res..

[69]  Kirk E. Hevener,et al.  Fragment-Based Drug Discovery Using a Multidomain, Parallel MD-MM/PBSA Screening Protocol , 2013, J. Chem. Inf. Model..

[70]  Glen E. P. Ropella,et al.  Cloud computing and validation of expandable in silico livers , 2010, BMC Systems Biology.

[71]  Diwakar Shukla,et al.  OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. , 2013, Journal of chemical theory and computation.

[72]  G. Degliesposti,et al.  Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening , 2009, Chemical biology & drug design.

[73]  Pierre-François Marteau,et al.  LNA: Fast Protein Structural Comparison Using a Laplacian Characterization of Tertiary Structure , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[74]  Margaret E. Johnson,et al.  Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.

[75]  Ying-Ta Wu,et al.  GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid , 2010, Journal of Grid Computing.

[76]  Vincent Breton,et al.  Design and Discovery of Plasmepsin II Inhibitors Using an Automated Workflow on Large‐Scale Grids , 2009, ChemMedChem.

[77]  Pu Liu,et al.  Accelerating Chemical Database Searching Using Graphics Processing Units , 2011, J. Chem. Inf. Model..

[78]  Duncan D. A. Ruiz,et al.  wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model , 2013, BioMed research international.

[79]  Thomas Ertl,et al.  GPU-powered tools boost molecular visualization , 2011, Briefings Bioinform..

[80]  Jingfa Xiao,et al.  Bioinformatics clouds for big data manipulation , 2012, Biology Direct.

[81]  Gábor Terstyánszky,et al.  Large‐scale virtual screening experiments on Windows Azure‐based cloud resources , 2014, Concurr. Comput. Pract. Exp..

[82]  Bairong Shen,et al.  Translational Biomedical Informatics in the Cloud: Present and Future , 2013, BioMed research international.

[83]  Ivan Janciak,et al.  Supporting Molecular Modeling Workflows within a Grid Services Cloud , 2010, ICCSA.

[84]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[85]  Thorsten Meinl,et al.  KNIME: The Konstanz Information Miner , 2007, GfKl.

[86]  Chao Ma,et al.  GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison , 2011, J. Chem. Inf. Model..

[87]  Barend Mons,et al.  Open PHACTS: semantic interoperability for drug discovery. , 2012, Drug discovery today.

[88]  Wataru Shinoda,et al.  Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics. , 2011, Journal of chemical theory and computation.

[89]  Todd J. Martínez,et al.  Generating Efficient Quantum Chemistry Codes for Novel Architectures. , 2013, Journal of chemical theory and computation.

[90]  Ming Sun,et al.  The impact of hardware improvement for molecular modeling in a grid environment , 2009, Expert opinion on drug discovery.

[91]  John J. Rehr,et al.  A high performance scientific cloud computing environment for materials simulations , 2012, Comput. Phys. Commun..

[92]  Julio Daniel Carvalho Maia,et al.  GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations. , 2012, Journal of chemical theory and computation.

[93]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[94]  Kai-Wei Chang,et al.  iScreen: world’s first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan , 2011, J. Comput. Aided Mol. Des..

[95]  Vijay S. Pande,et al.  Efficient nonbonded interactions for molecular dynamics on a graphics processing unit , 2010, J. Comput. Chem..

[96]  Christine M. Isborn,et al.  Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units , 2011, Journal of chemical theory and computation.

[97]  Andrey Asadchev,et al.  Fast and Flexible Coupled Cluster Implementation. , 2013, Journal of chemical theory and computation.