Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers.

[1]  R. Kubo.  GENERALIZED CUMULANT EXPANSION METHOD , 1962 .

[2]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[3]  S. Prager,et al.  Variational Treatment of Hydrodynamic Interaction in Polymers , 1969 .

[4]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[5]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[6]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[7]  W. C. Swope,et al.  A computer simulation method for the calculation of equilibrium constants for the formation of physi , 1981 .

[8]  B. Berne.  Modification of the overlap potential to mimic a linear site-site potential , 1981 .

[9]  P. Seetharamulu,et al.  A potential function for protein folding , 1991 .

[10]  S. Rackovsky,et al.  Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide , 1993, Protein science : a publication of the Protein Society.

[11]  S. Rackovsky,et al.  Calculation of protein backbone geometry from α‐carbon coordinates based on peptide‐group dipole alignment , 1993, Protein science : a publication of the Protein Society.

[12]  A. Godzik,et al.  A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins , 1993 .

[13]  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 .

[14]  G. Saretzki,et al.  Mild hyperoxia shortens telomeres and inhibits proliferation of fibroblasts: a model for senescence? , 1995, Experimental cell research.

[15]  P. Tavan,et al.  Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force , 1996, Science.

[16]  J. Shay,et al.  Telomerase activity in human germline and embryonic tissues and cells. , 1996, Developmental genetics.

[17]  Y. Okamoto,et al.  Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble , 1996, physics/9710018.

[18]  K. Dill,et al.  Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.

[19]  K. Kuwajima.  The molten globule state of α‐lactalbumin , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[20]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[21]  A. Ben-Naim.  STATISTICAL POTENTIALS EXTRACTED FROM PROTEIN STRUCTURES : ARE THESE MEANINGFUL POTENTIALS? , 1997 .

[22]  A. Liwo,et al.  A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data , 1997 .

[23]  Christodoulos A. Floudas,et al.  Prediction of Oligopeptide Conformations via Deterministic Global Optimization , 1997, J. Glob. Optim..

[24]  A. Liwo,et al.  United‐residue force field for off‐lattice protein‐structure simulations: III. Origin of backbone hydrogen‐bonding cooperativity in united‐residue potentials , 1998 .

[25]  S. Rackovsky,et al.  Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. , 1998, Biopolymers.

[26]  K. Dill,et al.  Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics , 1998, Proteins.

[27]  A. Malevanets,et al.  Mesoscopic model for solvent dynamics , 1999 .

[28]  A. Liwo,et al.  Calculation of protein conformation by global optimization of a potential energy function , 1999, Proteins.

[29]  A. Liwo,et al.  Protein structure prediction by global optimization of a potential energy function. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[30]  A. Liwo,et al.  Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[31]  H. Scheraga,et al.  Global optimization of clusters, crystals, and biomolecules. , 1999, Science.

[32]  A. Liwo,et al.  Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field , 2001 .

[33]  H. Scheraga,et al.  Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing , 2001 .

[34]  A. Liwo,et al.  A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[36]  Adam Liwo,et al.  Evolution of physics‐based methodology for exploring the conformational energy landscape of proteins , 2002, J. Comput. Chem..

[37]  Julian Lee,et al.  Full Optimization of Linear Parameters of a United Residue Protein Potential , 2002, cond-mat/0309486.

[38]  Peter G. Wolynes,et al.  Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach , 2002 .

[39]  Zaida Luthey-Schulten,et al.  Folding funnels: The key to robust protein structure prediction , 2002, J. Comput. Chem..

[40]  V. Pande,et al.  Multiplexed-replica exchange molecular dynamics method for protein folding simulation. , 2003, Biophysical journal.

[41]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[42]  P. Wolynes,et al.  Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach , 2003 .

[43]  H. Scheraga,et al.  Packing helices in proteins by global optimization of a potential energy function , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Skolnick,et al.  Reduced models of proteins and their applications , 2004 .

[45]  A. Liwo,et al.  Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems† , 2004 .

[46]  Alexander D. MacKerell.  Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..

[47]  R. Friesner,et al.  High‐resolution prediction of protein helix positions and orientations , 2004, Proteins.

[48]  A. Liwo,et al.  Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization , 2004 .

[49]  A. Kolinski.  Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.

[50]  M. Mayer,et al.  Hsp70 chaperones: Cellular functions and molecular mechanism , 2005, Cellular and Molecular Life Sciences.

[51]  A. Liwo,et al.  Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[52]  A. Liwo,et al.  Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. , 2005, The journal of physical chemistry. B.

[53]  A. Liwo,et al.  Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Hajime Tanaka.  Roles of hydrodynamic interactions in structure formation of soft matter: protein folding as an example , 2005 .

[55]  A. Liwo,et al.  Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. , 2005, The journal of physical chemistry. B.

[56]  A. Liwo,et al.  Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function. , 2006, The Journal of chemical physics.

[57]  A. Liwo,et al.  Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. , 2006, Journal of molecular biology.

[58]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[59]  A. Liwo,et al.  Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model. , 2007, The journal of physical chemistry. B.

[60]  A. Liwo,et al.  Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems. , 2007, The journal of physical chemistry. B.

[61]  A. Liwo,et al.  Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. , 2007, The journal of physical chemistry. B.

[62]  P. Derreumaux,et al.  A coarse‐grained protein force field for folding and structure prediction , 2007, Proteins.

[63]  P. Coveney,et al.  Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules. , 2007, The Journal of chemical physics.

[64]  A. Liwo,et al.  Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field. , 2007, Journal of chemical theory and computation.

[65]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[66]  G. Voth.  Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .

[67]  P. Lansdorp,et al.  Telomeres and Aging , 2008 .

[68]  A. Liwo,et al.  Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field , 2008 .

[69]  Yi He,et al.  United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding , 2009, J. Comput. Biol..

[70]  M. Cieplak,et al.  Hydrodynamic interactions in protein folding. , 2008, The Journal of chemical physics.

[71]  A. Elcock,et al.  Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins. , 2009, Journal of chemical theory and computation.

[72]  E. Zuiderweg,et al.  Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate , 2009, Proceedings of the National Academy of Sciences.

[73]  A. Liwo,et al.  Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. , 2009, Journal of chemical theory and computation.

[74]  A. Liwo,et al.  Principal component analysis for protein folding dynamics. , 2009, Journal of molecular biology.

[75]  Valentina Tozzini,et al.  Minimalist models for proteins: a comparative analysis , 2010, Quarterly Reviews of Biophysics.

[76]  A. Liwo,et al.  Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. , 2010, Journal of the American Chemical Society.

[77]  A. Liwo,et al.  Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. , 2010, Journal of molecular biology.

[78]  J. Bujnicki,et al.  Predicting Atomic Details of the Unfolding Pathway for YibK, a Knotted Protein from the SPOUT Superfamily , 2010, Journal of biomolecular structure & dynamics.

[79]  H. Kampinga,et al.  The HSP70 chaperone machinery: J proteins as drivers of functional specificity , 2010, Nature Reviews Molecular Cell Biology.

[80]  A. Elcock,et al.  Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association. , 2010, Biophysical journal.

[81]  A. Liwo,et al.  Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. , 2011, The journal of physical chemistry. B.

[82]  A. Liwo,et al.  PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. , 2011, Journal of molecular biology.

[83]  Sumudu P. Leelananda,et al.  Multibody coarse‐grained potentials for native structure recognition and quality assessment of protein models , 2011, Proteins.

[84]  A. Liwo,et al.  A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)). , 2011, The journal of physical chemistry. B.

[85]  A. Liwo,et al.  Coarse-Grained Models of Proteins: Theory and Applications , 2011 .

[86]  R. Kapral,et al.  Mesoscopic dynamics of diffusion-influenced enzyme kinetics. , 2011, The Journal of chemical physics.

[87]  Adam K. Sieradzan,et al.  Folding and self-assembly of a small protein complex. , 2012, Journal of chemical theory and computation.

[88]  A. Liwo,et al.  Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain. , 2012, Journal of molecular biology.

[89]  Adam K. Sieradzan,et al.  Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine. , 2012, Journal of chemical theory and computation.

[90]  Kaifu Gao,et al.  MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD , 2012 .

[91]  Nicholas P. Schafer,et al.  AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. , 2012, Journal of Physical Chemistry B.

[92]  Roman Kityk,et al.  Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. , 2012, Molecular cell.

[93]  Adam K. Sieradzan,et al.  Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. , 2012, Journal of chemical theory and computation.

[94]  Adam Liwo,et al.  Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. , 2012, Journal of chemical theory and computation.

[95]  A. Liwo,et al.  Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. , 2012, Journal of chemical theory and computation.

[96]  D. Tieleman,et al.  Perspective on the Martini model. , 2013, Chemical Society reviews.

[97]  J. Skolnick,et al.  On the importance of hydrodynamic interactions in lipid membrane formation. , 2013, Biophysical journal.

[98]  M. Feig,et al.  PRIMO: A Transferable Coarse-grained Force Field for Proteins. , 2013, Journal of chemical theory and computation.

[99]  A. Liwo,et al.  Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. , 2013, Physical review letters.

[100]  Benoît Roux,et al.  The Theory of Ultra-Coarse-Graining. 1. General Principles. , 2013, Journal of chemical theory and computation.

[101]  Adam K. Sieradzan,et al.  Lessons from application of the UNRES force field to predictions of structures of CASP10 targets , 2013, Proceedings of the National Academy of Sciences.

[102]  S. Cacchione,et al.  Chromatin Structure in Telomere Dynamics , 2013, Front. Oncol..

[103]  Marissa G. Saunders,et al.  Coarse-graining methods for computational biology. , 2013, Annual review of biophysics.

[104]  Helgi I Ingólfsson,et al.  The power of coarse graining in biomolecular simulations , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[105]  Adam K. Sieradzan,et al.  A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions , 2014, Journal of Molecular Modeling.

[106]  A. Liwo,et al.  Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements , 2014, Proceedings of the National Academy of Sciences.

[107]  Adam Liwo,et al.  WeFold: A coopetition for protein structure prediction , 2014, Proteins.

[108]  M. Feig,et al.  Recent advances in transferable coarse-grained modeling of proteins. , 2014, Advances in protein chemistry and structural biology.

[109]  Adam K. Sieradzan,et al.  Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field , 2014, Journal of chemical theory and computation.

[110]  Gregory A Voth,et al.  The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation. , 2014, Journal of chemical theory and computation.

[111]  Tadashi Ando,et al.  Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models , 2014, PLoS Comput. Biol..

[112]  A. Liwo,et al.  Molecular modeling of the binding modes of the iron‐sulfur protein to the Jac1 co‐chaperone from Saccharomyces cerevisiae by all‐atom and coarse‐grained approaches , 2015, Proteins.

[113]  A. Liwo,et al.  Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach. , 2015, The Journal of chemical physics.

[114]  Adam K. Sieradzan,et al.  Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions. , 2015, Journal of chemical theory and computation.

[115]  S. Melchionna,et al.  Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. , 2015, Journal of chemical theory and computation.

[116]  Adam K. Sieradzan,et al.  Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations. , 2015, Journal of chemical theory and computation.

[117]  Adam Liwo,et al.  A Maximum-Likelihood Approach to Force-Field Calibration , 2015, J. Chem. Inf. Model..

[118]  Adam Liwo,et al.  Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field , 2016, J. Chem. Inf. Model..

[119]  Adam K. Sieradzan,et al.  Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction. , 2016, The Journal of chemical physics.

[120]  Adam Liwo,et al.  Performance of protein-structure predictions with the physics-based UNRES force field in CASP11 , 2016, Bioinform..

[121]  A. Kolinski,et al.  Coarse-Grained Protein Models and Their Applications. , 2016, Chemical reviews.

[122]  James C. Robertson,et al.  Assessing the Current State of Amber Force Field Modifications for DNA , 2016, Journal of chemical theory and computation.

[123]  J. Bujnicki,et al.  SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction , 2015, Nucleic acids research.

[124]  A. Liwo,et al.  Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. , 2017, The journal of physical chemistry. B.

[125]  Adam K. Sieradzan,et al.  What Makes Telomeres Unique? , 2017, The journal of physical chemistry. B.

[126]  H. Scheraga,et al.  Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics. , 2017, ACS chemical neuroscience.

[127]  Adam K. Sieradzan,et al.  Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A. , 2017, Journal of chemical theory and computation.

[128]  A. Liwo,et al.  Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics , 2017, J. Chem. Inf. Model..

[129]  Adam K. Sieradzan,et al.  A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains. , 2017, The Journal of chemical physics.

[130]  A. Kolinski,et al.  SURPASS Low-Resolution Coarse-Grained Protein Modeling. , 2017, Journal of chemical theory and computation.

[131]  G. Papoian.  Coarse-Grained Modeling of Biomolecules , 2017 .

[132]  Adam Liwo,et al.  A new protein nucleic‐acid coarse‐grained force field based on the UNRES and NARES‐2P force fields , 2018, J. Comput. Chem..

[133]  Sylvain D. Vallet,et al.  Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners , 2018, Scientific Reports.

[134]  M. Makowski.  Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field , 2018, Springer Series on Bio- and Neurosystems.

[135]  Agnieszka S. Karczynska,et al.  Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets. , 2018, Journal of molecular graphics & modelling.

[136]  D. Wales,et al.  Computational Studies of the Mechanical Stability for Single-Strand Break DNA. , 2018, The journal of physical chemistry. B.

[137]  H. Scheraga,et al.  Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aβ. , 2018, The journal of physical chemistry. B.

[138]  Adam K. Sieradzan,et al.  Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing. , 2018, Physical chemistry chemical physics : PCCP.

[139]  Adam K. Sieradzan,et al.  Shielding effect in protein folding. , 2018, Journal of molecular graphics & modelling.

[140]  Adam Liwo,et al.  Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information , 2018, Proteins.

[141]  Adam Liwo,et al.  UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics , 2018, Nucleic Acids Res..

[142]  Adam Liwo,et al.  An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 , 2018, Scientific Reports.

[143]  A. Liwo,et al.  Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase , 2018, PloS one.

[144]  Nidhi Singh,et al.  Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications , 2019, International journal of molecular sciences.

[145]  A. Liwo,et al.  Local and long range potentials for heparin-protein systems for coarse-grained simulations. , 2019, Biopolymers.

[146]  Cezary Czaplewski,et al.  Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins , 2019 .

[147]  Adam K. Sieradzan,et al.  Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. , 2019, Journal of molecular graphics & modelling.

[148]  Adam K. Sieradzan,et al.  A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. , 2019, The Journal of chemical physics.

[149]  S. Pantano,et al.  The SIRAH 2.0 Force Field: Altius, Fortius, Citius. , 2019, Journal of chemical theory and computation.

[150]  Adam Liwo,et al.  Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints , 2019, J. Comput. Chem..