Blind testing of routine, fully automated determination of protein structures from NMR data

scientific article

Blind testing of routine, fully automated determination of protein structures from NMR data is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1016/J.STR.2012.01.002
P932PMC publication ID3609704
P698PubMed publication ID22325772
P5875ResearchGate publication ID221824213

P50authorCheryl ArrowsmithQ5092682
David BakerQ3814528
Harald SchwalbeQ15453283
Antonio RosatoQ40037625
Andrea GiachettiQ57307055
Geerten W VuisterQ61266630
Paolo RossiQ90658087
Michele VendruscoloQ28322492
Gaetano T. MontelioneQ28940908
Peter GüntertQ30158282
Torsten HerrmannQ30503909
Paul GuerryQ32415756
Aleksandras GutmanasQ32415758
Michael NilgesQ32417845
Wim F. VrankenQ37391332
P2093author name stringMichael A Kennedy
Gaohua Liu
Jurgen F Doreleijers
Alexandre M J J Bonvin
Andrea Cavalli
Hendrik R A Jonker
James M Aramini
Yuanpeng J Huang
Yunhuang Yang
Bin Wu
Oliver F Lange
Binchen Mao
Robert Vernon
Gijs van der Schot
Thérèse E Malliavin
Alexander Eletsky
Victor Jaravine
Anurag Bagaria
Yunfen He
Rajeswari Mani
Sjoerd de Vries
Thomas A Szyperski
P2860cites workThe Protein Data BankQ24515306
NMR structure determination for larger proteins using backbone-only dataQ24603298
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence dataQ24646326
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shiftsQ24651272
Consistent blind protein structure generation from NMR chemical shift dataQ24657929
LGA: A method for finding 3D similarities in protein structuresQ24672185
MolProbity: all-atom contacts and structure validation for proteins and nucleic acidsQ24684673
Traditional biomolecular structure determination by NMR spectroscopy allows for major errorsQ25257832
Flipping of alkylated DNA damage bridges base and nucleotide excision repairQ27655873
Version 1.2 of the Crystallography and NMR systemQ27860583
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANAQ27860611
Refinement of protein structures in explicit solventQ27860639
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMRQ27860778
Quantitative evaluation of experimental NMR restraints.Q44593564
Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structuresQ47388542
Determination of protein backbone structure using only residual dipolar couplingsQ49305511
Accurate NMR structures through minimization of an extended hybrid energy.Q51869415
Domain definition and target classification for CASP7Q56879564
Single-Step Determination of Protein Substructures Using Dipolar Couplings: Aid to Structural GenomicsQ57211407
Automated structure determination from NMR spectraQ82022661
Torsion angle dynamics for NMR structure calculation with the new program DYANAQ27860808
Recognition of errors in three-dimensional structures of proteinsQ28249658
ARIA2: automated NOE assignment and data integration in NMR structure calculationQ28275170
Evaluating protein structures determined by structural genomics consortiaQ29547577
RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBankQ29614749
Scoring function for automated assessment of protein structure template qualityQ29615862
VERIFY3D: assessment of protein models with three-dimensional profilesQ29615886
Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSAQ29616475
Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOSQ29617863
A topology-constrained distance network algorithm for protein structure determination from NOESY data.Q30352330
Automated protein structure determination from NMR spectra.Q30357194
Protein structure determination from NMR chemical shiftsQ30362013
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.Q30362842
The war of tools: how can NMR spectroscopists detect errors in their structures?Q30368080
Structural biology by NMR: structure, dynamics, and interactions.Q30372281
Advances in automated NMR protein structure determinationQ30400806
Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling dataQ30427834
Modeling errors in NOE data with a log-normal distribution improves the quality of NMR structuresQ31018635
Structure calculation of biological macromolecules from NMR data.Q31988286
Accurate automated protein NMR structure determination using unassigned NOESY dataQ33517696
The eNMR platform for structural biologyQ33794207
Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statisticsQ34392409
Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identificationsQ34436608
Weighting of experimental evidence in macromolecular structure determinationQ34478512
CASD-NMR: critical assessment of automated structure determination by NMRQ35000303
Force fields for protein simulationsQ35590728
The new program OPAL for molecular dynamics simulations and energy refinements of biological macromoleculesQ36831940
Ambiguous distance data in the calculation of NMR structuresQ36878828
P433issue2
P921main subjectautomationQ184199
P304page(s)227-236
P577publication date2012-02-01
P1433published inStructureQ15709970
P1476titleBlind testing of routine, fully automated determination of protein structures from NMR data
P478volume20

Reverse relations

cites work (P2860)
Q30394410A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions
Q30009993A unified NMR strategy for high-throughput determination of backbone fold of small proteins
Q30360709ALMOST: an all atom molecular simulation toolkit for protein structure determination.
Q30417560Accurate protein structure modeling using sparse NMR data and homologous structure information
Q38123436An overview of tools for the validation of protein NMR structures.
Q30374821Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3.
Q40881375Analysis of the structural quality of the CASD-NMR 2013 entries.
Q30356624Assessment of template-based protein structure predictions in CASP10
Q58483998Automated protein structure determination by NMR
Q58698459Automatic C chemical shift reference correction for unassigned protein NMR spectra
Q30374174CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.
Q41666652CING: an integrated residue-based structure validation program suite
Q91704782Chemical shift-based methods in NMR structure determination
Q30372955Combined automated NOE assignment and structure calculation with CYANA.
Q90902061Combining Evolutionary Covariance and NMR Data for Protein Structure Determination
Q30366493Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.
Q37090944Guiding automated NMR structure determination using a global optimization metric, the NMR DP score
Q36840483HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts
Q45019743Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker
Q41091068Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.
Q30659119Improving 3D structure prediction from chemical shift data
Q30352079MOTOR: model assisted software for NMR structure determination.
Q30372362NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
Q30387827NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia
Q28607677NMRFAM-SDF: a protein structure determination framework
Q27679247PDBStat: a universal restraint converter and restraint analysis software package for protein NMR
Q49331440POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins
Q30421203PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles.
Q30375879PPM_One: a static protein structure based chemical shift predictor.
Q47985206Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.
Q28607680Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR
Q29863696Physics-based method to validate and repair flaws in protein structures
Q30357564Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures
Q90653346Protein structure prediction assisted with sparse NMR data in CASP13
Q30353837Quality assessment of protein NMR structures.
Q36088395RPF: a quality assessment tool for protein NMR structures
Q24620570Recommendations of the wwPDB NMR Validation Task Force
Q30353637Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins.
Q45926282Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta.
Q30413306Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space
Q27677493Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods
Q38589790Structure and Dynamics of Intrinsically Disordered Proteins
Q30391464Structure of fully protonated proteins by proton-detected magic-angle spinning NMR
Q30372900Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA.
Q58753045Systematic mapping of free energy landscapes of a growing filamin domain during biosynthesis
Q34697654The role of structural bioinformatics resources in the era of integrative structural biology
Q36059190The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.
Q38675094Unraveling the meaning of chemical shifts in protein NMR.

Search more.