Coarse-grained modeling of RNA 3D structure.
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[1] John B. Shoven,et al. I , Edinburgh Medical and Surgical Journal.
[2] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[3] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.
[4] J. Devlin,et al. Urey-Bradley potential constants in dinitrogen trioxide , 1961 .
[5] W. Olson,et al. Spatial configurations of polynucleotide chains. III. Polydeoxyribonucleotides , 1972 .
[6] W. Olson,et al. Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond model , 1972, Biopolymers.
[7] P J Flory,et al. Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides , 1972, Biopolymers.
[8] W. Olson,et al. Configurational statistics of polynucleotide chains. A single virtual bond treatment. , 1975, Macromolecules.
[9] Wilma K. Olson,et al. Configurational Statistics of Polynucleotide Chains. An Updated Virtual Bond Model to Treat Effects of Base Stacking , 1980 .
[10] S. Papson,et al. “Model” , 1981 .
[11] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[12] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[13] Donald Geman,et al. Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images , 1984, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[14] Fred W. Glover,et al. Future paths for integer programming and links to artificial intelligence , 1986, Comput. Oper. Res..
[15] P. Kollman,et al. An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.
[16] B. Ganem. RNA world , 1987, Nature.
[17] J. Ponder,et al. An efficient newton‐like method for molecular mechanics energy minimization of large molecules , 1987 .
[18] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[19] Alan M. Ferrenberg,et al. New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.
[20] Alan M. Ferrenberg,et al. Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.
[21] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[22] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[23] J. Hearst,et al. Predicting the three-dimensional folding of transfer RNA with a computer modeling protocol. , 1991, Biochemistry.
[24] J E Hearst,et al. Computer modeling 16 S ribosomal RNA. , 1991, Journal of molecular biology.
[25] Berg,et al. Multicanonical ensemble: A new approach to simulate first-order phase transitions. , 1992, Physical review letters.
[26] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[27] K. Sharp,et al. Macroscopic models of aqueous solutions : biological and chemical applications , 1993 .
[28] S. Harvey,et al. Modeling large nucleic acids , 1993 .
[29] Manfred J. Sippl,et al. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures , 1993, J. Comput. Aided Mol. Des..
[30] S. Harvey,et al. Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques. , 1994, Biophysical journal.
[31] Stephen C. Harvey,et al. Utilization of shape data in molecular mechanics using a potential based on spherical harmonic surfaces , 1994, J. Comput. Chem..
[32] Jacek Klinowski,et al. Taboo Search: An Approach to the Multiple Minima Problem , 1995, Science.
[33] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[34] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[35] Shankar Kumar,et al. Multidimensional free‐energy calculations using the weighted histogram analysis method , 1995, J. Comput. Chem..
[36] B. Roux. The calculation of the potential of mean force using computer simulations , 1995 .
[37] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[38] S. Whittington,et al. Monte carlo study of the interacting self-avoiding walk model in three dimensions , 1996 .
[39] Y. Okamoto,et al. Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble , 1996, physics/9710018.
[40] Laxmikant V. Kalé,et al. NAMD: a Parallel, Object-Oriented Molecular Dynamics Program , 1996, Int. J. High Perform. Comput. Appl..
[41] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[42] T. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..
[43] A. Kidera,et al. Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides , 1997 .
[44] E. Westhof,et al. Hierarchy and dynamics of RNA folding. , 1997, Annual review of biophysics and biomolecular structure.
[45] S. Pongor,et al. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena. , 1998, Trends in biochemical sciences.
[46] B. D. Coleman,et al. The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes. , 1998, Biophysical journal.
[47] P. Kollman,et al. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .
[48] Wolfhard Janke,et al. Multicanonical Monte Carlo simulations , 1998 .
[49] A. Pyle,et al. Stepping through an RNA structure: A novel approach to conformational analysis. , 1998, Journal of molecular biology.
[50] R Samudrala,et al. A graph-theoretic algorithm for comparative modeling of protein structure. , 1998, Journal of molecular biology.
[51] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[52] D. Turner,et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.
[53] U H Hansmann,et al. New Monte Carlo algorithms for protein folding. , 1999, Current opinion in structural biology.
[54] Laxmikant V. Kale,et al. NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .
[55] I. Tinoco,et al. How RNA folds. , 1999, Journal of molecular biology.
[56] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[57] A. Warshel,et al. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study , 1999 .
[58] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[59] D. Case,et al. Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.
[60] J. Mccammon,et al. Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2). , 2000, Biophysical journal.
[61] J. Doudna. Structural genomics of RNA , 2000, Nature Structural Biology.
[62] Alexander D. MacKerell,et al. Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.
[63] V. Zhurkin,et al. Modeling DNA deformations. , 2000, Current opinion in structural biology.
[64] E. Westhof,et al. TectoRNA: modular assembly units for the construction of RNA nano-objects. , 2001, Nucleic acids research.
[65] Taboo search by successive confinement: surveying a potential energy surface. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.
[66] A. Laio,et al. Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[68] V. Pande,et al. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. , 2003, Biophysical journal.
[69] Z. Weng,et al. A novel shape complementarity scoring function for protein‐protein docking , 2003, Proteins.
[70] A Xayaphoummine,et al. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[71] A. ADoefaa,et al. ? ? ? ? f ? ? ? ? ? , 2003 .
[72] Z. Weng,et al. ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.
[73] W. B. Arendall,et al. RNA backbone is rotameric , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[74] Anna Marie Pyle,et al. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. , 2003, Nucleic acids research.
[75] J. Antosiewicz,et al. Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.
[76] Chris Oostenbrink,et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..
[77] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[78] J. Antosiewicz,et al. Constant-pH molecular dynamics simulations: a test case of succinic acid , 2004 .
[79] Alain Xayaphoummine,et al. Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots , 2005, Nucleic Acids Res..
[80] D. Thirumalai,et al. Mechanical unfolding of RNA hairpins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[81] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[82] Song Cao,et al. Predicting RNA folding thermodynamics with a reduced chain representation model. , 2005, RNA.
[83] Michael Levitt,et al. Describing RNA structure by libraries of clustered nucleotide doublets. , 2005, Journal of molecular biology.
[84] Klaus Schulten,et al. Computational Investigations of Biological Nanosystems , 2000 .
[85] Robert K Z Tan,et al. YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models. , 2006, Journal of chemical theory and computation.
[86] Changbong Hyeon,et al. Forced-unfolding and force-quench refolding of RNA hairpins. , 2006, Biophysical journal.
[87] Shi-jie Chen,et al. RNA helix stability in mixed Na+/Mg2+ solution. , 2007, Biophysical journal.
[88] I. Tinoco,et al. Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. , 2007, RNA.
[89] P. Cieplak,et al. Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin. , 2007, Journal of chemical theory and computation.
[90] V. Viasnoff,et al. Encoding folding paths of RNA switches , 2006, Nucleic acids research.
[91] Nils G Walter,et al. Molecular dynamics simulations of RNA: an in silico single molecule approach. , 2007, Biopolymers.
[92] D. Baker,et al. Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.
[93] Stephen Neidle,et al. Principles of nucleic acid structure , 2007 .
[94] Anna Marie Pyle,et al. Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure. , 2007, Journal of molecular biology.
[95] Andrew V. Colasanti,et al. Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA , 2009, Biophysical Reviews.
[96] A. Laederach,et al. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. , 2008, Current opinion in chemical biology.
[97] Ignacio Tinoco,et al. Characterization of the Mechanical Unfolding of RNA Pseudoknots , 2007, Journal of Molecular Biology.
[98] Cecilia Clementi,et al. Mapping folding energy landscapes with theory and experiment. , 2008, Archives of biochemistry and biophysics.
[99] Changbong Hyeon,et al. Minimal models for proteins and RNA from folding to function. , 2008, Progress in molecular biology and translational science.
[100] Feng Ding,et al. iFoldRNA: three-dimensional RNA structure prediction and folding , 2008, Bioinform..
[101] F. Ding,et al. Ab initio folding of proteins with all-atom discrete molecular dynamics. , 2008, Structure.
[102] F. Major,et al. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.
[103] Magdalena A. Jonikas,et al. Structural inference of native and partially folded RNA by high-throughput contact mapping , 2008, Proceedings of the National Academy of Sciences.
[104] S. Whitelam,et al. The role of collective motion in examples of coarsening and self-assembly. , 2008, Soft matter.
[105] Hervé Isambert,et al. The jerky and knotty dynamics of RNA. , 2009, Methods.
[106] E. Sambriski,et al. Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[107] Kanti V. Mardia,et al. A Probabilistic Model of RNA Conformational Space , 2009, PLoS Comput. Biol..
[108] Feng Ding,et al. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. , 2009, Journal of the American Chemical Society.
[109] Piero Fariselli,et al. A graph theoretic approach to protein structure selection , 2009, Artif. Intell. Medicine.
[110] J. Šponer,et al. Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. , 2009, Methods.
[111] A. Warshel,et al. Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.
[112] W. Dawson,et al. Modeling the Chain Entropy of Biopolymers: Unifying Two Different Random Walk Models under One Framework , 2009 .
[113] Russ B. Altman,et al. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models , 2009, Bioinform..
[114] Magdalena A. Jonikas,et al. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. , 2009, RNA.
[115] Timothy C Elston,et al. Multiscale approaches for studying energy transduction in dynein. , 2009, Physical chemistry chemical physics : PCCP.
[116] Valentina Tozzini,et al. Minimalist models for proteins: a comparative analysis , 2010, Quarterly Reviews of Biophysics.
[117] Shi-Jie Chen,et al. Predicting loop-helix tertiary structural contacts in RNA pseudoknots. , 2010, RNA.
[118] Pengyu Y. Ren,et al. Coarse-grained model for simulation of RNA three-dimensional structures. , 2010, The journal of physical chemistry. B.
[119] Feng Ding,et al. On the significance of an RNA tertiary structure prediction. , 2010, RNA.
[120] Sandro Bottaro,et al. Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized , 2010, PloS one.
[121] Adam Liwo,et al. Coarse‐grained model of nucleic acid bases , 2010, J. Comput. Chem..
[122] Valentina Tozzini,et al. Multiscale modeling of proteins. , 2010, Accounts of chemical research.
[123] J. Šponer,et al. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? , 2010, The journal of physical chemistry. B.
[124] Alexander D. MacKerell,et al. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. , 2010, Journal of chemical theory and computation.
[125] D. Baker,et al. Atomic accuracy in predicting and designing non-canonical RNA structure , 2010, Nature Methods.
[126] D. Jost,et al. Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model. , 2010, The Journal of chemical physics.
[127] K. Réblová,et al. Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome , 2010, Nucleic acids research.
[128] P. Derreumaux,et al. HiRE-RNA: a high resolution coarse-grained energy model for RNA. , 2010, The journal of physical chemistry. B.
[129] J. Doye,et al. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. , 2010, The Journal of chemical physics.
[130] Arieh Warshel,et al. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. , 2011, Annual review of physical chemistry.
[131] Kristian Rother,et al. RNA and protein 3D structure modeling: similarities and differences , 2011, Journal of molecular modeling.
[132] A. Stuchebrukhov,et al. Accounting for electronic polarization in non-polarizable force fields. , 2011, Physical chemistry chemical physics : PCCP.
[133] Shi-Jie Chen,et al. Physics-based de novo prediction of RNA 3D structures. , 2011, The journal of physical chemistry. B.
[134] Tobin R Sosnick,et al. The folding of single domain proteins--have we reached a consensus? , 2011, Current opinion in structural biology.
[135] Ryuhei Harada,et al. Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method. , 2011, The journal of physical chemistry. B.
[136] Adelene Y. L. Sim,et al. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. , 2011, RNA.
[137] T. Schlick,et al. Computational approaches to RNA structure prediction, analysis, and design. , 2011, Current opinion in structural biology.
[138] Pengyu Y. Ren,et al. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. , 2011, Journal of chemical theory and computation.
[139] A. Ansari,et al. Fast folding of RNA pseudoknots initiated by laser temperature-jump. , 2011, Journal of the American Chemical Society.
[140] Charles L. Brooks,et al. Surveying implicit solvent models for estimating small molecule absolute hydration free energies , 2011, J. Comput. Chem..
[141] Marc A. Martí-Renom,et al. All-atom knowledge-based potential for RNA structure prediction and assessment , 2011, Bioinform..
[142] Adelene Y. L. Sim,et al. Modeling and design by hierarchical natural moves , 2012, Proceedings of the National Academy of Sciences.
[143] D. Turner,et al. Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes. , 2012, Physical chemistry chemical physics : PCCP.
[144] Feng Ding,et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. , 2012, RNA.
[145] A. Serganov,et al. Molecular recognition and function of riboswitches. , 2012, Current opinion in structural biology.
[146] K. Réblová,et al. Structure and mechanical properties of the ribosomal L1 stalk three-way junction , 2012, Nucleic acids research.
[147] Adelene Y. L. Sim,et al. Modeling nucleic acids. , 2012, Current opinion in structural biology.
[148] Shi-Jie Chen,et al. Predicting ion-nucleic acid interactions by energy landscape-guided sampling. , 2012, Journal of chemical theory and computation.
[149] Jennifer L. Knight,et al. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. , 2012, Journal of chemical theory and computation.
[150] Jérôme Waldispühl,et al. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure , 2012, Bioinform..
[151] Loren Dean Williams,et al. Cations in charge: magnesium ions in RNA folding and catalysis. , 2012, Current opinion in structural biology.
[152] D. Tieleman,et al. Perspective on the Martini model. , 2013, Chemical Society reviews.
[153] Michal Otyepka,et al. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. , 2013, Methods.
[154] P. Derreumaux,et al. Coarse-grained simulations of RNA and DNA duplexes. , 2013, The journal of physical chemistry. B.
[155] A. Liwo,et al. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. , 2013, Physical review letters.
[156] Michal Otyepka,et al. Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment. , 2013, Biopolymers.
[157] Jennifer L. Knight,et al. pH-dependent dynamics of complex RNA macromolecules. , 2013, Journal of chemical theory and computation.
[158] W G Noid,et al. Systematic methods for structurally consistent coarse-grained models. , 2013, Methods in molecular biology.
[159] W G Noid,et al. Perspective: Coarse-grained models for biomolecular systems. , 2013, The Journal of chemical physics.
[160] A. Serganov,et al. A Decade of Riboswitches , 2013, Cell.
[161] D Thirumalai,et al. Coarse-grained model for predicting RNA folding thermodynamics. , 2013, The journal of physical chemistry. B.
[162] Francisco Melo,et al. WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures , 2013, Bioinform..
[163] Pengyu Ren,et al. RNA 3D structure prediction by using a coarse-grained model and experimental data. , 2013, The journal of physical chemistry. B.
[164] J. Doye,et al. DNA hybridization kinetics: zippering, internal displacement and sequence dependence , 2013, Nucleic acids research.
[165] W F Drew Bennett,et al. Improved Parameters for the Martini Coarse-Grained Protein Force Field. , 2013, Journal of chemical theory and computation.
[166] H. Gong,et al. A novel implicit solvent model for simulating the molecular dynamics of RNA. , 2013, Biophysical journal.
[167] Kentaro Shimizu,et al. A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations , 2013 .
[168] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[169] Marissa G. Saunders,et al. Coarse-graining methods for computational biology. , 2013, Annual review of biophysics.
[170] Flavio Romano,et al. A nucleotide-level coarse-grained model of RNA. , 2014, The Journal of chemical physics.
[171] Marco Biasini,et al. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10 , 2014, Proteins.
[172] Franca Fraternali,et al. Design and application of implicit solvent models in biomolecular simulations , 2014, Current opinion in structural biology.
[173] Shi-jie Chen,et al. Exploring the electrostatic energy landscape for tetraloop-receptor docking. , 2014, Physical chemistry chemical physics : PCCP.
[174] A. Liwo,et al. DNA Duplex Formation with a Coarse-Grained Model , 2014, Journal of chemical theory and computation.
[175] Hashim M. Al-Hashimi,et al. Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges , 2014, The journal of physical chemistry. B.
[176] Zhiping Weng,et al. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers , 2014, Bioinform..
[177] C. Brooks,et al. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism , 2014, Proteins.
[178] Stefano Piana,et al. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. , 2014, Current opinion in structural biology.
[179] Janusz M Bujnicki,et al. Computational modeling of RNA 3D structures, with the aid of experimental restraints , 2014, RNA biology.
[180] A. Laederach,et al. Mapping the Kinetic Barriers of a Large RNA Molecule's Folding Landscape , 2014, PloS one.
[181] Anna Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP) — round x , 2014, Proteins.
[182] M. D. Carbajal-Tinoco,et al. RNA pseudo-knots simulated with a one-bead coarse-grained model. , 2014, The Journal of chemical physics.
[183] T. Cheatham,et al. Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). , 2015, Biochimica et biophysica acta.
[184] Namhee Kim,et al. Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach. , 2015, Methods in enzymology.
[185] Yasuteru Shigeta,et al. Simple, yet powerful methodologies for conformational sampling of proteins. , 2015, Physical chemistry chemical physics : PCCP.
[186] Rhiju Das,et al. Modeling complex RNA tertiary folds with Rosetta. , 2015, Methods in enzymology.
[187] I. Hofacker,et al. Predicting RNA 3D structure using a coarse-grain helix-centered model , 2015, RNA.
[188] Yasuteru Shigeta,et al. Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini‐protein, chignolin , 2015, J. Comput. Chem..
[189] Robert C. Harris,et al. Examining the assumptions underlying continuum-solvent models. , 2015, Journal of chemical theory and computation.
[190] Hsien-Da Huang,et al. RNAcentral: an international database of ncRNA sequences , 2014, Nucleic Acids Res..
[191] N. Dokholyan,et al. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models. , 2015, Methods in enzymology.
[192] Feng Ding,et al. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures , 2015, RNA.
[193] Janusz M Bujnicki,et al. Computational modeling of RNA 3D structures and interactions. , 2016, Current opinion in structural biology.
[194] J. Bujnicki,et al. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction , 2015, Nucleic acids research.