Oleg Sobolev Publications

  1. van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW: Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure 2021, [PMID: 33823127] [PMCID: PMC8349848]


  1. Wang L, Kruse H, Sobolev OV, Moriarty NW, Waller MP, Afonine PV, Biczysko M: Real-space quantum-based refinement for cryo-EM: Q|R#3. Acta Cryst. 2020, 76:1184-1191
  2. Sobolev OV, Afonine PV, Moriarty NW, Hekkelman ML, Joosten RP, Perrakis A, Adams PD: A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. Structure 2020, 28:1249-1258.e2. [PMID: 32857966] [PMCID: PMC7642142]

  1. Terwilliger TC, Adams PD, Afonine PV, Sobolev OV: Cryo-EM map interpretation and protein model-building using iterative map segmentation. Protein Sci. 2019, [PMID: 31599033] [PMCID: PMC6933853]
  2. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Cryst. 2019, 75:861-877 [PMID: 31588918] [PMCID: PMC6778852 ]
  3. Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K: Cryo_fit: Democratization of flexible fitting for cryo-EM. J Struct Biol. 2019, 208:1-6 [PMID: 31279069] [PMCID: ]
  4. Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY: Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Cryst. 2019, D75:451-454. [PMID: 30988261] [PMCID: PMC6465986]

  1. Terwilliger TC, Adams PD, Afonine PV, Sobolev OV: A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. Nat Methods 2018, 15:905-908. [PMID: 30377346] [PMCID: ]
  2. Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A: New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Cryst. 2018, D74:814-840. [PMID: 30198894] [PMCID: PMC6130467]
  3. Terwilliger TC, Adams PD, Afonine PV, Sobolev OV: Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. J. Struct. Biol. 2018, 204:338-343 [PMID: 30063987] [PMCID: PMC6163059]
  4. Terwilliger TC, Sobolev OV, Afonine PV, Adams PD: Automated map sharpening by maximization of detail and connectivity. Acta Cryst 2018, D74:545-559. [PMID: 29872005] [PMCID: PMC6096490]
  5. Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD: Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst 2018, D74:531-544. [PMID: 29872004] [PMCID: PMC6096492]

  1. Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD: Polder maps: improving OMIT maps by excluding bulk solvent. Acta Cryst. 2017, D73:148-157 [PMID: 28177311] [PMCID: PMC5297918]
  1. Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A. Programming new geometry restraints: parallelity of atomic groups. J. Appl .Cryst. 2015, 48. 1130-1141. [PMID: ] [PMCID: ]
  2. Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. FEM: feature-enhanced map. Acta Cryst. 2015, D71.646-666. [PMID: 25760612] [PMCID: ]
  3. Sobolev OV, Moriarty NW, Afonine PV, Hintze BJ, Richardson DC, Richardson JS & Adams PD. Disulfide bond restraints. Computational Crystallography Newsletter. 6. 13.
  1. Sobolev OV, Afonine PV & Adams PD. Connectivity analysis tools in CCTBX. Computational Crystallography Newsletter. 5. 35-37.
  1. Sobolev OV. Detection of alternative conformations: Shift_plot and AC_prediction programs. J. Appl. Cryst. 46. 554-559.
  1. Sobolev OV, and Lunin VY. Detection of alternative conformations by unrestrained refinement. Acta Cryst. D68. 1118-1127.
  2. Sobolev OV. DETAC: tools to detect alternative conformations by unrestrained refinement. Computational Crystallography Newsletter. 3. 32-34.
  3. Sobolev OV , Lunin VY. The use of Refmac crystallographic refinement program for the detection of alternative conformations in biological macromolecules. Mathematical Biology and Bioinformatics. 7. t16-t24.


  1. Sobolev OV, Lunina NL, Lunin VY. The use of cluster analysis methods for the study of a set of feasible solutions of the phase problem in biological crystallography. Computer Research and Modeling. 2. 91-101 (in Russian).


  1. Sobolev OV, Lunin VY. Unrestrained reciprocal space refinement of macromolecular structures as a tool to indicate alternative conformations. Mathematical Biology and Bioinformatics. 3. 50-59 (in Russian).


  1. Sobolev EV, Sobolev OV, Tikhonov DA. Online resource for theoretical study of hydration of biopolymers. SAR and QSAR in Environmental Research. 19. 303-315.