Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Privacy-aware community infrastructureResearch graph
References from Coarse-grained (hybrid) integrative modeling of biomolecular interactions. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1002/pmic.200700131
10.1002/pmic.200700131 · External reference
10.1016/j.cell.2019.05.016
10.1016/j.cell.2019.05.016 · External reference
Unresolved reference
2019 · External reference
10.1146/annurev-biochem-013118-111429
10.1146/annurev-biochem-013118-111429 · External reference
10.1016/j.cell.2018.03.014
10.1016/j.cell.2018.03.014 · External reference
Symposium on Three-Dimensional Structure of Macromolecules of Biological Origin. By Invitation of the Committee on Arrangements for the Autumn Meeting. Presented before the Academy on October 19, 1966. Chairman, Walter Kauzmann
1967 · External reference
10.1002/anie.201403689
10.1002/anie.201403689 · External reference
10.1038/253694a0
10.1038/253694a0 · External reference
How to fold graciously
1969 · External reference
Principles of protein-protein recognition
10.1038/256705a0 · 1975 · External reference
Computer analysis of protein-protein interaction
10.1016/0022-2836(78)90302-9 · 1978 · External reference
10.1002/anie.198404673
10.1002/anie.198404673 · External reference
10.1021/acs.chemrev.6b00163
10.1021/acs.chemrev.6b00163 · External reference
A lattice statistical mechanics model of the conformational and sequence spaces of proteins
10.1021/ma00200a030 · 1989 · External reference
10.1002/pro.5560040401
10.1002/pro.5560040401 · External reference
Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
10.1006/jmbi.1994.1110 · 1994 · External reference
The folding mechanism of larger model proteins: Role of native structure
10.1073/pnas.93.16.8356 · 1996 · External reference
10.1073/pnas.161438898
10.1073/pnas.161438898 · External reference
Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
10.1006/jmbi.2001.5266 · 2002 · External reference
10.1016/j.polymer.2003.10.064
10.1016/j.polymer.2003.10.064 · External reference
10.1002/prot.340180405
10.1002/prot.340180405 · External reference
10.1021/ja036959e
10.1021/ja036959e · External reference
10.1002/prot.22645
10.1002/prot.22645 · External reference
10.1021/jp102497y
10.1021/jp102497y · External reference
10.1021/ct5007746
10.1021/ct5007746 · External reference
10.1021/ct900653p
10.1021/ct900653p · External reference
10.1021/ct100379f
10.1021/ct100379f · External reference
10.1021/jp071097f
10.1021/jp071097f · External reference
10.1021/ct700324x
10.1021/ct700324x · External reference
10.1021/jp9058966
10.1021/jp9058966 · External reference
10.1021/jp402615p
10.1021/jp402615p · External reference
10.1021/ct900313w
10.1021/ct900313w · External reference
Polarizable water model for the coarse-grained MARTINI force field
10.1371/journal.pcbi.1000810 · 2010 · External reference
10.1021/ct3009655
10.1021/ct3009655 · External reference
10.1021/acs.jctc.5b00286
10.1021/acs.jctc.5b00286 · External reference
10.1016/j.bpj.2017.05.043
10.1016/j.bpj.2017.05.043 · External reference
10.1021/jp5105938
10.1021/jp5105938 · External reference
10.1021/ct300646g
10.1021/ct300646g · External reference
Perspective: Coarse-grained models for biomolecular systems
2013 · External reference
Coarse-graining methods for computational biology
10.1146/annurev-biophys-083012-130348 · 2013 · External reference
Interatomic potentials from first-principles calculations: The force-matching method
10.1209/0295-5075/26/8/005 · 1994 · External reference
10.1063/1.1739396
10.1063/1.1739396 · External reference
10.1021/jp044629q
10.1021/jp044629q · External reference
Empirical potential Monte Carlo simulation of fluid structure
10.1016/0301-0104(95)00357-6 · 1996 · External reference
Fitting coarse-grained distribution functions through an iterative force-matching method
10.1063/1.4811667 · 2013 · External reference
Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins
10.1063/1.5138991 · 2020 · External reference
The power of coarse graining in biomolecular simulations Wiley Interdisciplinary Reviews
10.1002/wcms.1169 · 2014 · External reference
10.1201/9781315374284-7
10.1201/9781315374284-7 · External reference
Force fields for coarse-grained molecular simulations from a corresponding states correlation
10.1021/ie404247e · 2014 · External reference
10.1146/annurev-chembioeng-061312-103314
10.1146/annurev-chembioeng-061312-103314 · External reference
Evaluation of the SAFT-γ Mie force field with solvation free energy calculations
10.1016/j.fluid.2018.11.018 · 2019 · External reference
10.1038/s41586-019-1923-7
10.1038/s41586-019-1923-7 · External reference
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
10.1002/prot.25834 · 2019 · External reference
Critical assessment of methods of protein structure prediction (CASP) – Round XIII
10.1002/prot.25823 · 2019 · External reference
10.1021/acs.jpcc.6b10908
10.1021/acs.jpcc.6b10908 · External reference
10.1021/acscentsci.8b00913
10.1021/acscentsci.8b00913 · External reference
Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining
10.1063/1.5097559 · 2019 · External reference
Machine learning coarse grained models for water
10.1038/s41467-018-08222-6 · 2019 · External reference
Multiscale modeling of biomolecular systems: in serial and in parallel
10.1016/j.sbi.2007.03.004 · 2007 · External reference
10.1021/ct401118k
10.1021/ct401118k · External reference
Computationally efficient multiscale reactive molecular dynamics to describe amino acid deprotonation in proteins
10.1021/acs.jctc.5b01109 · 2016 · External reference
Computer simulation of liquids
10.2307/2938686 · 1991 · External reference
Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations
10.1021/jp076142y · 2008 · External reference
Hybrid simulations: Combining atomistic and coarse-grained force fields using virtual sites
10.1039/c0cp02981e · 2011 · External reference
10.1021/ct2004275
10.1021/ct2004275 · External reference
Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides
10.1002/jcc.24694 · 2017 · External reference
Mixing MARTINI: Electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations
10.1021/jp311533p · 2013 · External reference
10.1021/acs.jctc.7b00840
10.1021/acs.jctc.7b00840 · External reference
LightDock goes information-driven
10.1093/bioinformatics/btz642 · 2020 · External reference
Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1
10.1002/prot.25198 · 2017 · External reference
10.1021/ja026939x
10.1021/ja026939x · External reference
10.1107/s0907444998003254
10.1107/s0907444998003254 · External reference
10.1021/acs.jctc.9b00310
10.1021/acs.jctc.9b00310 · External reference
10.1002/prot.24400
10.1002/prot.24400 · External reference
The pepATTRACT web server for blind, large-scale peptide-protein docking
10.1093/nar/gkx335 · 2017 · External reference
Protein-DNA docking with a coarse-grained force field
10.1186/1471-2105-13-228 · 2012 · External reference
Protein modeling and structure prediction with a reduced representation
10.18388/abp.2004_3575 · 2004 · External reference
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
10.1093/nar/gkv456 · 2015 · External reference
10.1093/bioinformatics/btw141
10.1093/bioinformatics/btw141 · External reference
InterEvScore: A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution
10.1093/bioinformatics/btt260 · 2013 · External reference
10.1093/nar/gky377
10.1093/nar/gky377 · External reference
Pairwise and multimeric protein–protein docking using the lzerd program suite
10.1007/978-1-4939-0366-5_15 · 2014 · External reference
Modeling disordered protein interactions from biophysical principles
10.1371/journal.pcbi.1005485 · 2017 · External reference
Identification of protein interaction partners and protein-protein interaction sites
10.1016/j.jmb.2008.08.002 · 2008 · External reference
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
10.1093/nar/gkaa015 · 2020 · External reference
10.1002/prot.22797
10.1002/prot.22797 · External reference
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
10.1016/s0022-2836(03)00670-3 · 2003 · External reference
Unresolved reference
2019 · External reference
CLUB-MARTINI: Selecting favourable interactions amongst available candidates, a coarse-grained simulation approach to scoring docking decoys
2016 · External reference
DOCK/PIERR: Web server for structure prediction of protein-protein complexes
10.1007/978-1-4939-0366-5_14 · 2014 · External reference
Prediction of protein structure and interaction by GALAXY protein modeling programs
2014 · External reference
10.1093/nar/gkv495
10.1093/nar/gkv495 · External reference
LightDock: A new multi-scale approach to protein-protein docking
2018 · External reference
10.1007/978-3-642-34123-6_16
10.1007/978-3-642-34123-6_16 · External reference
MEGADOCK 4.0: An ultra-high-performance protein-protein docking software for heterogeneous supercomputers
10.1093/bioinformatics/btu532 · 2014 · External reference
Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls
10.1002/jcc.23538 · 2014 · External reference
The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures
10.1093/bioinformatics/btw756 · 2017 · External reference
pyDockWEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring
10.1093/bioinformatics/btt262 · 2013 · External reference
PyDockCG: New coarse-grained potential for protein-protein docking
10.1021/jp112292b · 2011 · External reference
VORFFIP-driven dock: V-D2OCK, a fast, accurate protein docking strategy
10.1371/journal.pone.0118107 · 2015 · External reference
10.1371/journal.pbio.1001244
10.1371/journal.pbio.1001244 · External reference
10.1002/pro.3311
10.1002/pro.3311 · External reference
10.1016/j.jmb.2015.09.014
10.1016/j.jmb.2015.09.014 · External reference
MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
10.3389/fmolb.2019.00102 · 2019 · External reference
10.1016/j.csbj.2019.12.007 · Admitted local publication
10.1021/ct400617g
10.1021/ct400617g · External reference
SIRAH tools: Mapping, backmapping and visualization of coarse-grained models
10.1093/bioinformatics/btw020 · 2016 · External reference
Software news and update reconstruction of atomistic details from coarse-grained structures
10.1002/jcc.21415 · 2010 · External reference
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
10.1110/ps.0239303 · 2003 · External reference
Reconstruction of atomistic structures from coarse-grained models for Protein-DNA complexes
10.1021/acs.jctc.7b00954 · 2018 · External reference
10.1002/prot.21371
10.1002/prot.21371 · External reference
10.1093/bioinformatics/btv740
10.1093/bioinformatics/btv740 · External reference
10.1107/s0907444911054515
10.1107/s0907444911054515 · External reference
10.1021/acs.jctc.9b00062
10.1021/acs.jctc.9b00062 · External reference
10.1016/j.sbi.2013.07.006
10.1016/j.sbi.2013.07.006 · External reference
Integrative computational modeling of protein interactions
10.1111/febs.12771 · 2014 · External reference
10.3390/genes9090432
10.3390/genes9090432 · External reference
A series of PDB related databases for everyday needs
10.1093/nar/gkq1105 · 2011 · External reference
10.1093/nar/gku1028
10.1093/nar/gku1028 · External reference
10.1016/j.str.2015.05.013
10.1016/j.str.2015.05.013 · External reference
Federating structural models and data: outcomes from a workshop on archiving integrative structures
10.1016/j.str.2019.11.002 · 2019 · External reference
Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex
10.1074/mcp.m114.041673 · 2014 · External reference
10.1038/nmeth.3617
10.1038/nmeth.3617 · External reference
Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modeling
10.1074/mcp.m115.056473 · 2016 · External reference
Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex
10.1038/s41467-018-06953-0 · 2018 · External reference
10.1038/s41594-018-0118-5
10.1038/s41594-018-0118-5 · External reference
10.1074/jbc.m117.803619
10.1074/jbc.m117.803619 · External reference
10.1073/pnas.1915542117
10.1073/pnas.1915542117 · External reference
Molecular architecture of the yeast Mediator complex
10.7554/elife.08719 · 2015 · External reference
10.1016/j.str.2019.06.006
10.1016/j.str.2019.06.006 · External reference
10.1016/j.str.2018.12.004
10.1016/j.str.2018.12.004 · External reference
10.1038/s41594-019-0259-1
10.1038/s41594-019-0259-1 · External reference
10.1085/jgp.201611679
10.1085/jgp.201611679 · External reference
10.1016/j.str.2017.12.015
10.1016/j.str.2017.12.015 · External reference
10.1038/nature26003
10.1038/nature26003 · External reference
10.1002/pro.3235
10.1002/pro.3235 · External reference
