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References from Homology modeling in the time of collective and artificial intelligence. Local targets link to admitted publications; unresolved targets remain external evidence.
Linus Pauling’s quest for the structure of proteins
10.1007/s11224-009-9565-2 · 2009 · External reference
Homology modeling in drug discovery: Overview, current applications, and future perspectives
10.1111/cbdd.13388 · 2019 · External reference
Conformational sampling techniques
10.2174/13816128113199990603 · 2014 · External reference
A large-scale experiment to assess protein structure prediction methods
10.1002/prot.340230303 · 1995 · External reference
10.1147/rd.33.0210
10.1147/rd.33.0210 · External reference
Machine learning: applications of artificial intelligence to imaging and diagnosis
10.1007/s12551-018-0449-9 · 2019 · External reference
Artificial intelligence (AI) in healthcare and biomedical research: Why a strong computational/AI bioethics framework is required?
10.4103/ijo.ijo_1292_18 · 2019 · External reference
Introduction to artificial intelligence in medicine
10.1080/13645706.2019.1575882 · 2019 · External reference
Brief introduction of medical database and data mining technology in big data era
10.1111/jebm.12373 · 2020 · External reference
10.1016/j.csbj.2014.11.005
10.1016/j.csbj.2014.11.005 · External reference
ProteinNet: a standardized data set for machine learning of protein structure
10.1186/s12859-019-2932-0 · 2019 · External reference
Recent Progress in Machine Learning-based Prediction of Peptide Activity for Drug Discovery
10.2174/1568026619666190122151634 · 2019 · External reference
10.1146/annurev.biophys.29.1.291
10.1146/annurev.biophys.29.1.291 · External reference
10.1002/prot.21662
10.1002/prot.21662 · External reference
Homology Modeling: an Overview of Fundamentals and Tools
2017 · External reference
Ten quick tips for homology modeling of high-resolution protein 3D structures
10.1371/journal.pcbi.1007449 · 2020 · External reference
Homology Modeling in Drug Discovery-an Update on the Last Decade
2017 · External reference
10.1016/j.str.2013.08.007
10.1016/j.str.2013.08.007 · External reference
Structure-based virtual screening for drug discovery: a problem-centric review
10.1208/s12248-012-9322-0 · 2012 · External reference
10.1016/j.bpj.2016.02.001
10.1016/j.bpj.2016.02.001 · External reference
Cryo-electron microscopy targets in CASP13: Overview and evaluation of results
10.1002/prot.25817 · 2019 · External reference
Computational methods for constructing protein structure models from 3D electron microscopy maps
10.1016/j.jsb.2013.06.008 · 2013 · External reference
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement
10.1016/j.jmb.2010.01.041 · 2010 · External reference
10.1038/s41586-020-2833-4
10.1038/s41586-020-2833-4 · External reference
10.1038/nmeth.1818
10.1038/nmeth.1818 · External reference
Hidden Markov model speed heuristic and iterative HMM search procedure
10.1186/1471-2105-11-431 · 2010 · External reference
10.1093/nar/25.17.3389
10.1093/nar/25.17.3389 · External reference
10.1107/s2059798317008920
10.1107/s2059798317008920 · External reference
Homology modeling in drug discovery: current trends and applications
10.1016/j.drudis.2009.04.006 · 2009 · External reference
10.1093/bioinformatics/btm404
10.1093/bioinformatics/btm404 · External reference
The EMBL-EBI bioinformatics web and programmatic tools framework
10.1093/nar/gkv279 · 2015 · External reference
10.1093/nar/gkh340
10.1093/nar/gkh340 · External reference
10.1093/bioinformatics/btr292
10.1093/bioinformatics/btr292 · External reference
Template-based protein structure modeling
10.1007/978-1-60761-842-3_6 · 2010 · External reference
Advances in homology protein structure modeling
10.2174/138920306777452312 · 2006 · External reference
Side-chain modeling with an optimized scoring function
10.1110/ps.24902 · 2002 · External reference
10.1021/acs.jctc.9b00309
10.1021/acs.jctc.9b00309 · External reference
10.1002/prot.22488
10.1002/prot.22488 · External reference
10.1093/bioinformatics/btaa234
10.1093/bioinformatics/btaa234 · External reference
Protein structure modeling and refinement by global optimization in CASP12
10.1002/prot.25426 · 2018 · External reference
CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL
10.1002/prot.24399 · 2014 · External reference
10.1142/9789814449144_0008
10.1142/9789814449144_0008 · External reference
10.1093/nar/gkg571
10.1093/nar/gkg571 · External reference
Progress over the first decade of CASP experiments
10.1002/prot.20740 · 2005 · External reference
10.1093/nar/gki524
10.1093/nar/gki524 · External reference
10.1093/bioinformatics/16.9.776
10.1093/bioinformatics/16.9.776 · External reference
Unresolved reference
2015 · External reference
10.1006/jmbi.1997.0994
10.1006/jmbi.1997.0994 · External reference
CAD-score: a new contact area difference-based function for evaluation of protein structural models
10.1002/prot.24172 · 2013 · External reference
10.1093/nar/gkh398
10.1093/nar/gkh398 · External reference
10.1016/0263-7855(90)80070-v
10.1016/0263-7855(90)80070-v · External reference
10.1107/s0021889892009944
10.1107/s0021889892009944 · External reference
QMEAN: A comprehensive scoring function for model quality assessment
10.1002/prot.21715 · 2008 · External reference
10.1110/ps.062416606
10.1110/ps.062416606 · External reference
10.1002/prot.340170404
10.1002/prot.340170404 · External reference
MetaMQAP: a meta-server for the quality assessment of protein models
10.1186/1471-2105-9-403 · 2008 · External reference
10.1110/ps.062095806
10.1110/ps.062095806 · External reference
Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes
2020 · External reference
Homology modeling of human GABA-AT and devise some novel and potent inhibitors via computer-aided drug design techniques
2020 · External reference
10.1186/1758-2946-4-17
10.1186/1758-2946-4-17 · External reference
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective
10.1002/elps.200900140 · 2009 · External reference
10.1016/j.jmb.2018.01.013
10.1016/j.jmb.2018.01.013 · External reference
Biomolecules in the computer: Jmol to the rescue
10.1002/bmb.2006.494034042644 · 2006 · External reference
Structural insight into the ligand-receptor interaction between glycyrrhetinic acid (GA) and the high-mobility group protein B1 (HMGB1)-DNA complex
10.6026/97320630081147 · 2012 · External reference
Molden: a pre- and post-processing program for molecular and electronic structures
10.1023/a:1008193805436 · 2000 · External reference
10.1002/bmb.20966
10.1002/bmb.20966 · External reference
RASMOL: biomolecular graphics for all
10.1016/s0968-0004(00)89080-5 · 1995 · External reference
SAMSON: a software package for the biopolymer primary structure analysis
1995 · External reference
10.1007/s00894-017-3489-3
10.1007/s00894-017-3489-3 · External reference
10.1002/jcc.20084
10.1002/jcc.20084 · External reference
10.1016/0263-7855(96)00018-5
10.1016/0263-7855(96)00018-5 · External reference
10.1016/0263-7855(90)80070-v
10.1016/0263-7855(90)80070-v · External reference
10.1007/978-1-4939-7366-8_4
10.1007/978-1-4939-7366-8_4 · External reference
10.1006/jmbi.1993.1626
10.1006/jmbi.1993.1626 · External reference
Comparative Protein Structure Modeling Using MODELLER
10.1002/cpbi.3 · 2016 · External reference
10.1002/elps.1150181505
10.1002/elps.1150181505 · External reference
10.1093/bioinformatics/bti770
10.1093/bioinformatics/bti770 · External reference
10.1093/nar/gku340
10.1093/nar/gku340 · External reference
10.1093/nar/gkg520
10.1093/nar/gkg520 · External reference
I-TASSER server for protein 3D structure prediction
10.1186/1471-2105-9-40 · 2008 · External reference
10.1038/nprot.2010.5
10.1038/nprot.2010.5 · External reference
10.1038/nprot.2009.2
10.1038/nprot.2009.2 · External reference
10.1038/nprot.2015.053
10.1038/nprot.2015.053 · External reference
10.1002/prot.10629
10.1002/prot.10629 · External reference
10.1038/nprot.2012.085
10.1038/nprot.2012.085 · External reference
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
2012 · External reference
GalaxyWEB server for protein structure prediction and refinement
10.1093/nar/gks493 · 2012 · External reference
AlphaFold at CASP13
10.1093/bioinformatics/btz422 · 2019 · External reference
All are not equal: a benchmark of different homology modeling programs
10.1110/ps.041253405 · 2005 · External reference
An evaluation of automated homology modelling methods at low target template sequence similarity
10.1093/bioinformatics/btm262 · 2007 · External reference
10.1529/biophysj.106.082313
10.1529/biophysj.106.082313 · External reference
10.1007/978-3-642-19968-4_3
10.1007/978-3-642-19968-4_3 · External reference
The Wisdom of the Crowd in Combinatorial Problems
10.1111/j.1551-6709.2011.01223.x · 2012 · External reference
10.7717/peerj.6762
10.7717/peerj.6762 · External reference
Crowdsourcing in health and medical research: a systematic review
10.1186/s40249-020-0622-9 · 2020 · External reference
10.1088/1741-2560/5/1/p01
10.1088/1741-2560/5/1/p01 · External reference
10.3389/fnbot.2018.00034
10.3389/fnbot.2018.00034 · External reference
COMPUTING: Screen Savers of the World Unite!
10.1126/science.290.5498.1903 · 2000 · External reference
10.1109/tpds.2006.110
10.1109/tpds.2006.110 · External reference
Unresolved reference
External reference
Better together: Elements of successful scientific software development in a distributed collaborative community
10.1371/journal.pcbi.1007507 · 2020 · External reference
10.1038/nature09304
10.1038/nature09304 · External reference
10.1038/s41586-019-1274-4
10.1038/s41586-019-1274-4 · External reference
Building de novo cryo-electron microscopy structures collaboratively with citizen scientists
10.1371/journal.pbio.3000472 · 2019 · External reference
10.1126/science.1219021
10.1126/science.1219021 · External reference
10.1016/j.sbi.2005.05.011
10.1016/j.sbi.2005.05.011 · External reference
Critical assessment of methods of protein structure prediction (CASP)-Round XIII
10.1002/prot.25823 · 2019 · External reference
10.1021/acs.jpcb.9b02102
10.1021/acs.jpcb.9b02102 · External reference
Contact order and ab initio protein structure prediction
10.1110/ps.3790102 · 2002 · External reference
Progress over the first decade of CASP experiments
10.1002/prot.20740 · 2005 · External reference
Progress from CASP6 to CASP7
10.1002/prot.21769 · 2007 · External reference
CASP10 results compared to those of previous CASP experiments
10.1002/prot.24448 · 2014 · External reference
10.1002/prot.25064
10.1002/prot.25064 · External reference
10.1002/prot.25415
10.1002/prot.25415 · External reference
Critical assessment of methods of protein structure prediction (CASP)—Round XIII
10.1002/prot.25823 · 2019 · External reference
Analysis of distance-based protein structure prediction by deep learning in CASP13
10.1002/prot.25810 · 2019 · External reference
10.1002/prot.25792
10.1002/prot.25792 · External reference
Prediction of protein oligomer structures using GALAXY in CASP13
10.1002/prot.25814 · 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
10.1093/nar/gkz322
10.1093/nar/gkz322 · External reference
10.1093/nar/gkz367
10.1093/nar/gkz367 · External reference
Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
10.1093/bioinformatics/bty1037 · 2019 · External reference
10.1002/prot.25697
10.1002/prot.25697 · External reference
10.1007/978-1-0716-0708-4_2
10.1007/978-1-0716-0708-4_2 · External reference
10.1002/prot.25784
10.1002/prot.25784 · External reference
Unresolved reference
External reference
10.1016/0301-4622(95)00120-4
10.1016/0301-4622(95)00120-4 · External reference
10.1016/j.csbj.2019.12.011
10.1016/j.csbj.2019.12.011 · External reference
DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure
2019 · External reference
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
10.1371/journal.pcbi.1005324 · 2017 · External reference
10.1002/prot.25798
10.1002/prot.25798 · External reference
Unresolved reference
External reference
Deep clustering of protein folding simulations
10.1186/s12859-018-2507-5 · 2018 · External reference
Unresolved reference
External reference
10.1021/acs.chemrev.6b00440
10.1021/acs.chemrev.6b00440 · External reference
10.12688/f1000research.22907.1
10.12688/f1000research.22907.1 · External reference
Unresolved reference
External reference
10.1016/b978-0-12-816034-3.00007-9
10.1016/b978-0-12-816034-3.00007-9 · 2020 · External reference
10.1016/b978-0-12-816034-3.00007-9
10.1016/b978-0-12-816034-3.00007-9 · External reference
Assessing the accuracy of contact predictions in CASP13
10.1002/prot.25819 · 2019 · External reference
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
10.1093/bioinformatics/btr638 · 2011 · External reference
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
10.1073/pnas.1314045110 · 2013 · External reference
FreeContact: fast and free software for protein contact prediction from residue co-evolution
10.1186/1471-2105-15-85 · 2014 · External reference
CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations
10.1093/bioinformatics/btu500 · 2014 · External reference
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning
2019 · External reference
10.1093/bioinformatics/btu791
10.1093/bioinformatics/btu791 · External reference
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
10.1371/journal.pcbi.1003889 · 2014 · External reference
Improving accuracy of protein contact prediction using balanced network deconvolution
10.1002/prot.24744 · 2015 · External reference
R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter
10.1093/bioinformatics/btw181 · 2016 · External reference
10.1371/journal.pcbi.1005324
10.1371/journal.pcbi.1005324 · External reference
10.1016/j.cels.2017.11.014
10.1016/j.cels.2017.11.014 · External reference
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
10.1093/bioinformatics/bty341 · 2018 · External reference
10.1093/bioinformatics/bty481
10.1093/bioinformatics/bty481 · External reference
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks
10.1093/bioinformatics/btz291 · 2019 · External reference
10.1002/prot.25779
10.1002/prot.25779 · External reference
DESTINI: A deep-learning approach to contact-driven protein structure prediction
2019 · External reference
10.1186/s12859-017-1713-x
10.1186/s12859-017-1713-x · External reference
PconsC4: fast, free, easy, and accurate contact predictions
10.1093/bioinformatics/bty1036 · 2018 · External reference
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks
10.1093/bioinformatics/btx781 · 2018 · External reference
The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome
10.1155/2010/568068 · 2010 · External reference
Structural Disorder in Eukaryotes
10.1371/journal.pone.0034687 · 2012 · External reference
The relationship between proteome size, structural disorder and organism complexity
10.1186/gb-2011-12-12-r120 · 2011 · External reference
Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree
10.1002/pro.2864 · 2016 · External reference
10.1016/j.bbapap.2012.12.008
10.1016/j.bbapap.2012.12.008 · External reference
Intrinsically disordered proteins in PubMed: what can the tip of the iceberg tell us about what lies below?
10.1039/c5ra24866c · 2016 · External reference
10.1016/j.tibs.2012.08.004
10.1016/j.tibs.2012.08.004 · External reference
Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics
10.3389/fphy.2019.00010 · 2019 · External reference
The protein non-folding problem: amino acid determinants of intrinsic order and disorder
2001 · External reference
10.1111/j.1742-4658.2010.07684.x
10.1111/j.1742-4658.2010.07684.x · External reference
Paradoxes and wonders of intrinsic disorder: Complexity of simplicity
2016 · External reference
10.1074/jbc.r115.685859
10.1074/jbc.r115.685859 · External reference
10.1016/j.sbi.2011.04.001
10.1016/j.sbi.2011.04.001 · External reference
10.1073/pnas.0909644106
10.1073/pnas.0909644106 · External reference
10.1038/nature09450
10.1038/nature09450 · External reference
10.1002/prot.20446
10.1002/prot.20446 · External reference
Prediction of disorder with new computational tool: BVDEA
10.1016/j.eswa.2011.04.160 · 2011 · External reference
The Prediction of Intrinsically Disordered Proteins Based on Feature Selection
2019 · External reference
The Ising model for prediction of disordered residues from protein sequence alone
10.1088/1478-3975/8/3/035004 · 2011 · External reference
SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method
10.1080/073911012010525022 · 2012 · External reference
Improved Disorder Prediction by Combination of Orthogonal Approaches
10.1371/journal.pone.0004433 · 2009 · External reference
A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction
10.1093/bib/bbx126 · 2017 · External reference
10.1101/2020.08.11.245852
10.1101/2020.08.11.245852 · External reference
Assessment of protein disorder region predictions in CASP10
10.1002/prot.24391 · 2014 · External reference
10.1002/prot.23161
10.1002/prot.23161 · External reference
10.1093/bioinformatics/btv092
10.1093/bioinformatics/btv092 · External reference
10.1016/j.bpj.2015.03.051
10.1016/j.bpj.2015.03.051 · External reference
Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation
10.1371/journal.pone.0107353 · 2014 · External reference
10.1145/3319619.3322002
10.1145/3319619.3322002 · External reference
Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains
10.1038/s41467-018-06034-2 · 2018 · External reference
SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data
10.1002/prot.25865 · 2020 · External reference
10.1073/pnas.1905068116
10.1073/pnas.1905068116 · External reference
10.1038/nmeth.3437
10.1038/nmeth.3437 · External reference
10.1007/978-3-319-94463-0
10.1007/978-3-319-94463-0 · External reference
