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Nikolay Dokholyan

Research Profile

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Physiology

Protein Folding

Chemicals & Drugs

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Thermodynamics

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Amino Acid Sequences

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Protein Denaturation

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Publications

TOP 3
Elizabeth A Proctor; Pradeep Kota; Justin A Caravella; Stephen J Demarest; Nikolay V Dokholyan
Highly covarying residues have a functional role in antibody constant domains.
Onur Dagliyan; Feng Ding; Srinivas N Chandrasekaran; Lanette Fee; Christina M Freisinger; Klaus M Hahn; Anna Huttenlocher; Andrei Karginov; David Shirvanyants; Gromoslaw A Smolen; Nikolay V Dokholyan
Rational design of a ligand-controlled protein conformational switch.
P Andrew Chong; Nikolay V Dokholyan; Pradeep Kota; Julie D Forman-Kay
Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability.

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2013: Elizabeth A Proctor; Pradeep Kota; Justin A Caravella; Stephen J Demarest; Nikolay V Dokholyan
Highly covarying residues have a functional role in antibody constant domains.
Proteins 2013;81(5):884-95.
2013: Onur Dagliyan; Feng Ding; Srinivas N Chandrasekaran; Lanette Fee; Christina M Freisinger; Klaus M Hahn; Anna Huttenlocher; Andrei Karginov; David Shirvanyants; Gromoslaw A Smolen; Nikolay V Dokholyan
Rational design of a ligand-controlled protein conformational switch.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(17):6800-4.
2013: P Andrew Chong; Nikolay V Dokholyan; Pradeep Kota; Julie D Forman-Kay
Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability.
Cold Spring Harbor perspectives in medicine 2013;3(3):a009522.
2013: Srinivas Ramachandran; Montserrat Samsó; Le Xu; Asima Chakraborty; Nikolay V Dokholyan; Yingwu Mei; Gerhard Meissner
Structural determinants of skeletal muscle ryanodine receptor gating.
The Journal of biological chemistry 2013;288(9):6154-65.
2013: Elizabeth A Proctor; Pradeep Kota; Justin A Caravella; Stephen J Demarest; Nikolay V Dokholyan
Metric to distinguish closely related domain families using sequence information.
Journal of molecular biology 2013;425(3):475-8.
2013: Lihua He; Tim Jensen; Pradeep Kota; Andrei A Aleksandrov; Liying Cui; Nikolay V Dokholyan; John R Riordan
Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2013;27(2):536-45.
2013: Christopher W Leonard; David H Mathews; Nikolay V Dokholyan; Oleg V Favorov; Christine E Hajdin; Fethullah Karabiber; Kevin M Weeks
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.
Biochemistry 2013;52(4):588-95.
2013: Srinivas Ramachandran; Kevin M Weeks; Feng Ding; Nikolay V Dokholyan
Statistical analysis of SHAPE-directed RNA secondary structure modeling.
Biochemistry 2013;52(4):596-9.
2012: Daud I Cole; Feng Ding; Nikolay V Dokholyan; Jason D Legassie; Vijay G Sekaran; Laura N Bonifacio; Michael B Jarstfer
New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling.
Journal of the American Chemical Society 2012;134(49):20070-80.
2012: Srinivas Ramachandran; Brenda Temple; Anastassia N Alexandrova; Stephen G Chaney; Nikolay V Dokholyan
Recognition of platinum-DNA adducts by HMGB1a.
Biochemistry 2012;51(38):7608-17.
2012: Feng Ding; Furukawa Yoshiaki; Nobuyuki Nukina; Nikolay V Dokholyan
Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates.
Journal of molecular biology 2012;421(4-5):548-60.
2012: Manuel Sparta; Feng Ding; Nikolay V Dokholyan; David Shirvanyants; Anastassia N Alexandrova
Hybrid dynamics simulation engine for metalloproteins.
Biophysical journal 2012;103(4):767-76.
2012: David Shirvanyants; Douglas Tsao; Feng Ding; Srinivas Ramachandran; Nikolay V Dokholyan
Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization.
The journal of physical chemistry. B 2012;116(29):8375-82.
2012: Nikolay V Dokholyan
Physical microscopic model of proteins under force.
The journal of physical chemistry. B 2012;116(23):6806-9.
2012: Feng Ding; Christopher A Lavender; Kevin M Weeks; Nikolay V Dokholyan
Three-dimensional RNA structure refinement by hydroxyl radical probing.
Nature methods 2012;9(6):603-8.
2012: Andrei A Aleksandrov; Luba Aleksandrov; Alexey E Alekseev; Liying Cui; Nikolay V Dokholyan; Martina Gentzsch; Lihua He; Tim Jensen; Pradeep Kota; Santiago Reyes; John R Riordan
Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR.
Journal of molecular biology 2012;419(1-2):41-60.
2012: Pradeep Kota; Monroe Stutts; Hong Dang; Agustin García-Caballero; Martina Gentzsch; Nikolay V Dokholyan
Energetic and structural basis for activation of the epithelial sodium channel by matriptase.
Biochemistry 2012;51(16):3460-9.
2012: Jui-Hua Hsieh; Shubin Liu; Xiang S Wang; Shuangye Yin; Nikolay V Dokholyan; Alexander Tropsha
Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening.
Journal of chemical information and modeling 2012;52(1):16-28.
2012: Douglas Tsao; Jeffrey S Wieskopf; Nikolay V Dokholyan; William Maixner; Jeffrey S Mogil; Naim Rashid; Rachel L Redler; Samantha K Segall; Robert E Sorge; Luda Diatchenko
Serotonin-induced hypersensitivity via inhibition of catechol O-methyltransferase activity.
Molecular pain 2012;8():25.
2012: Rachel L Redler; Nikolay V Dokholyan
The complex molecular biology of amyotrophic lateral sclerosis (ALS).
Progress in molecular biology and translational science 2012;107():215-62.
2012: Nagesh Pulicherla; Nikolay V Dokholyan; Pradeep Kota; Aravind Asokan
Intra- and inter-subunit disulfide bond formation is nonessential in adeno-associated viral capsids.
PloS one 2012;7(2):e32163.
2011: Gergely Gyimesi; Pradeep Kota; Srinivas Ramachandran; Balázs Sarkadi; Nikolay V Dokholyan; Tamás Hegedus
ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions.
Biochimica et biophysica acta 2011;1808(12):2954-64.
2011: Adrian W R Serohijos; Shuangye Yin; Feng Ding; Nikolay V Dokholyan; Josee Gauthier; Dustin G Gibson; William Maixner; Luda Diatchenko
Structural basis for μ-opioid receptor binding and activation.
Structure (London, England : 1993) 2011;19(11):1683-90.
2011: Jui-Hua Hsieh; Shubin Liu; Alexander Sedykh; Nikolay V Dokholyan; Shuangye Yin; Alexander Tropsha
Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets.
Journal of chemical information and modeling 2011;51(9):2027-35.
2011: Rachel L Redler; Kyle C Wilcox; Michael Caplow; Lanette Fee; Elizabeth A Proctor; Nikolay V Dokholyan
Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers.
Biochemistry 2011;50(32):7057-66.
2011: Pradeep Kota; Srinivas Ramachandran; Feng Ding; Nikolay V Dokholyan
Gaia: automated quality assessment of protein structure models.
Bioinformatics (Oxford, England) 2011;27(16):2209-15.
2011: Douglas Tsao; Nikolay V Dokholyan; Josée Gauthier; Svetlana A Shabalina; Luda Diatchenko
Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant.
Nucleic acids research 2011;39(14):6201-12.
2011: Denis Tsygankov; Adrian Wendil Serohijos; Nikolay V Dokholyan; Timothy C Elston
A physical model reveals the mechanochemistry responsible for dynein's processive motion.
Biophysical journal 2011;101(1):144-50.
2011: Elizabeth A Proctor; Feng Ding; Nikolay V Dokholyan
Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase.
Journal of molecular biology 2011;408(3):555-67.
2011: David Shirvanyants; Anastassia N Alexandrova; Nikolay V Dokholyan
Rigid substructure search.
Bioinformatics (Oxford, England) 2011;27(9):1327-9.
2011: Shuangye Yin; Nikolay V Dokholyan
Fingerprint-based structure retrieval using electron density.
Proteins 2011;79(3):1002-9.
2011: Pradeep Kota; Nikolay V Dokholyan
Approaches for probing the sequence space of substrates recognized by molecular chaperones.
Methods (San Diego, Calif.) 2011;53(3):318-24.
2011: Andrei V Karginov; Pradeep Kota; David Shirvanyants; Douglas D Young; Yan Zou; Nikolay V Dokholyan; Klaus M Hahn; Alexander Deiters
Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP.
Journal of the American Chemical Society 2011;133(3):420-3.
2011: Douglas Tsao; Luda Diatchenko; Nikolay V Dokholyan
Structural mechanism of S-adenosyl methionine binding to catechol O-methyltransferase.
PloS one 2011;6(8):e24287.
2011: Debadeep Bhattacharyya; Gunnar Boysen; Sharon L Campbell; Nikolay V Dokholyan; Candice L King; Wimal Pathmasiri; Srinivas Ramachandran; Shantanu Sharma; James A Swenberg; Irene Baskerville-Abraham; Stephen G Chaney
Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links.
PloS one 2011;6(8):e23582.
2011: Adrian W R Serohijos; Patrick H Thibodeau; Nikolay V Dokholyan
Molecular modeling tools and approaches for CFTR and cystic fibrosis.
Methods in molecular biology (Clifton, N.J.) 2011;741():347-63.
2011: Hamid Hadi-Alijanvand; Maryam Rouhani; Elizabeth A Proctor; Nikolay V Dokholyan; Ali A Moosavi-Movahedi
A folding pathway-dependent score to recognize membrane proteins.
PloS one 2011;6(3):e16778.
2011: Srinivas Ramachandran; Lisa Vogel; Brian D Strahl; Nikolay V Dokholyan
Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation.
PLoS computational biology 2011;7(1):e1001042.
2011: Srinivas Ramachandran; Pradeep Kota; Feng Ding; Nikolay V Dokholyan
Automated minimization of steric clashes in protein structures.
Proteins 2011;79(1):261-70.
2010: Feng Ding; Shuangye Yin; Nikolay V Dokholyan
Rapid flexible docking using a stochastic rotamer library of ligands.
Journal of chemical information and modeling 2010;50(9):1623-32.
2010: Andrei A Aleksandrov; Pradeep Kota; Luba Aleksandrov; Lihua He; Tim Jensen; Liying Cui; Martina Gentzsch; Nikolay V Dokholyan; John R Riordan
Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR.
Journal of molecular biology 2010;401(2):194-210.
2010: Ramesh K Jha; Andrew Leaver-Fay; Shuangye Yin; Yibing Wu; Glenn L Butterfoss; Thomas Szyperski; Nikolay V Dokholyan; Brian Kuhlman
Computational design of a PAK1 binding protein.
Journal of molecular biology 2010;400(2):257-70.
2010: Andrei Karginov; Feng Ding; Pradeep Kota; Nikolay V Dokholyan; Klaus M Hahn
Engineered allosteric activation of kinases in living cells.
Nature biotechnology 2010;28(7):743-7.
2010: Christine E Hajdin; Feng Ding; Nikolay V Dokholyan; Kevin M Weeks
On the significance of an RNA tertiary structure prediction.
RNA (New York, N.Y.) 2010;16(7):1340-9.
2010: Christopher A Lavender; Feng Ding; Nikolay V Dokholyan; Kevin M Weeks
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain.
Biochemistry 2010;49(24):4931-3.
2010: Erol A Gaillard; Pradeep Kota; Martina Gentzsch; Nikolay V Dokholyan; Monroe Stutts; Robert Tarran
Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases.
Pflügers Archiv : European journal of physiology 2010;460(1):1-17.
2010: Douglas Tsao; Nikolay V Dokholyan
Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity.
Physical chemistry chemical physics : PCCP 2010;12(14):3491-500.
2010: Vinal V Lakhani; Feng Ding; Nikolay V Dokholyan
Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences.
PLoS computational biology 2010;6(4):e1000772.
2010: Barry A Kesner; Sharon L Milgram; Brenda Temple; Nikolay V Dokholyan
Isoform divergence of the filamin family of proteins.
Molecular biology and evolution 2010;27(2):283-95.
2010: Douglas Tsao; Allen P Minton; Nikolay V Dokholyan
A didactic model of macromolecular crowding effects on protein folding.
PloS one 2010;5(8):e11936.
2010: Shuangye Yin; Feng Ding; Nikolay V Dokholyan
Computational evaluation of protein stability change upon mutations.
Methods in molecular biology (Clifton, N.J.) 2010;634():189-201.
2010: Barry A Kesner; Feng Ding; Brenda Temple; Nikolay V Dokholyan
N-terminal strands of filamin Ig domains act as a conformational switch under biological forces.
Proteins 2010;78(1):12-24.
2009: Shuangye Yin; Elizabeth A Proctor; Alexey A Lugovskoy; Nikolay V Dokholyan
Fast screening of protein surfaces using geometric invariant fingerprints.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(39):16622-6.
2009: Pradeep Kota; Daniel W Summers; Hong-Yu Ren; Doug Cyr; Nikolay V Dokholyan
Identification of a consensus motif in substrates bound by a Type I Hsp40.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(27):11073-8.
2009: Adrian Wendil Serohijos; Denis Tsygankov; Shubin Liu; Timothy C Elston; Nikolay V Dokholyan
Multiscale approaches for studying energy transduction in dynein.
Physical chemistry chemical physics : PCCP 2009;11(24):4840-50.
2009: Kyle C Wilcox; Li Zhou; Joshua K Jordon; Yi Huang; Yanbao Yu; Rachel L Redler; Xian Chen; Michael Caplow; Nikolay V Dokholyan
Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis.
The Journal of biological chemistry 2009;284(20):13940-7.
2009: Srinivas Ramachandran; Brenda Temple; Stephen G Chaney; Nikolay V Dokholyan
Structural basis for the sequence-dependent effects of platinum-DNA adducts.
Nucleic acids research 2009;37(8):2434-48.
2009: Srinivas Ramachandran; Adrian Wendil Serohijos; Le Xu; Gerhard Meissner; Nikolay V Dokholyan
A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1).
PLoS computational biology 2009;5(4):e1000367.
2009: Matthew P Torres; Michael J Lee; Feng Ding; Carrie Purbeck; Brian Kuhlman; Nikolay V Dokholyan; Henrik G Dohlman
G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase.
The Journal of biological chemistry 2009;284(13):8940-50.
2009: costin gherghe; Christopher W Leonard; Feng Ding; Nikolay V Dokholyan; Kevin M Weeks
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics.
Journal of the American Chemical Society 2009;131(7):2541-6.
2009: Torsten Schwede; Andrej Sali; Barry Honig; Michael Levitt; Helen M Berman; David Jones; Steven E Brenner; Stephen K Burley; Rhiju Das; Nikolay V Dokholyan; Roland Dunbrack; Krzysztof Fidelis; András Fiser; Adam Godzik; Yuanpeng Janet Huang; Christine Humblet; Matthew P Jacobson; Andrzej Joachimiak; Stanley R Krystek; Tanja Kortemme; Andriy Kryshtafovych; Gaetano T Montelione; John Moult; Diana Murray; Roberto Sanchez; Tobin R Sosnick; Daron M Standley; Terry Stouch; Sandor Vajda; Max Vasquez; John D Westbrook; Ian A Wilson
Outcome of a workshop on applications of protein models in biomedical research.
Structure (London, England : 1993) 2009;17(2):151-9.
2009: Evgeniy V Petrotchenko; Kunhong Xiao; Jennifer Cable; Yiwen Chen; Nikolay V Dokholyan; Christoph H Borchers
BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics.
Molecular & cellular proteomics : MCP 2009;8(2):273-86.
2009: Denis Tsygankov; Adrian Wendil Serohijos; Nikolay V Dokholyan; Timothy C Elston
Kinetic models for the coordinated stepping of cytoplasmic dynein.
The Journal of chemical physics 2009;130(2):025101.
2009: Gerhard Meissner; Daniel A Pasek; Naohiro Yamaguchi; Srinivas Ramachandran; Nikolay V Dokholyan; Ashutosh Tripathy
Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels.
Proteins 2009;74(1):207-11.
2008: Feng Ding; Nikolay V Dokholyan
Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(50):19696-701.
2008: Lihua He; Andrei A Aleksandrov; Adrian Wendil Serohijos; Tamás Hegedus; Luba A Aleksandrov; Liying Cui; Nikolay V Dokholyan; John R Riordan
Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating.
The Journal of biological chemistry 2008;283(39):26383-90.
2008: Csilla Ozvegy-Laczka; Rozália Laczkó; Csilla Hegedus; Thomas Litman; György Várady; Katalin Goda; Tamás Hegedus; Nikolay V Dokholyan; Brian P Sorrentino; András Váradi; Balázs Sarkadi
Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter.
The Journal of biological chemistry 2008;283(38):26059-70.
2008: Shantanu Sharma; Feng Ding; Nikolay V Dokholyan
iFoldRNA: three-dimensional RNA structure prediction and folding.
Bioinformatics (Oxford, England) 2008;24(17):1951-2.
2008: Shuangye Yin; Lada Biedermannova; Jiri Vondrasek; Nikolay V Dokholyan
MedusaScore: an accurate force field-based scoring function for virtual drug screening.
Journal of chemical information and modeling 2008;48(8):1656-62.
2008: Yiwen Chen; Nikolay V Dokholyan
Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm.
Molecular biology and evolution 2008;25(8):1530-3.
2008: Feng Ding; Douglas Tsao; Huifen Nie; Nikolay V Dokholyan
Ab initio folding of proteins with all-atom discrete molecular dynamics.
Structure (London, England : 1993) 2008;16(7):1010-8.
2008: Feng Ding; Shantanu Sharma; Poornima Chalasani; Vadim V Demidov; Natalia E Broude; Nikolay V Dokholyan
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.
RNA (New York, N.Y.) 2008;14(6):1164-73.
2008: Tamás Hegedus; Adrian Wendil Serohijos; Nikolay V Dokholyan; Lihua He; John R Riordan
Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR.
Journal of molecular biology 2008;378(5):1052-63.
2008: Adrian Wendil Serohijos; Tamás Hegedus; Andrei A Aleksandrov; Lihua He; Liying Cui; Nikolay V Dokholyan; John R Riordan
Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(9):3256-61.
2008: Adrian Wendil Serohijos; Tamás Hegedus; John R Riordan; Nikolay V Dokholyan
Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding.
PLoS computational biology 2008;4(2):e1000008.
2008: Jihua Hao; Adrian Wendil Serohijos; Gail Newton; Gina Tassone; Zuncai Wang; Dennis C Sgroi; Nikolay V Dokholyan; James P Basilion
Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers.
PLoS computational biology 2008;4(8):e1000138.
2008: Denise G Teotico; Monica L Frazier; Feng Ding; Nikolay V Dokholyan; Brenda Temple; Matthew R Redinbo
Active nuclear receptors exhibit highly correlated AF-2 domain motions.
PLoS computational biology 2008;4(7):e1000111.
2008: Shantanu Sharma; Feng Ding; Nikolay V Dokholyan
Probing protein aggregation using discrete molecular dynamics.
Frontiers in bioscience : a journal and virtual library 2008;13():4795-808.
2008: Shantanu Sharma; Nikolay V Dokholyan
DNA sequence mediates nucleosome structure and stability.
Biophysical journal 2008;94(1):1-3.
2008: Yiwen Chen; Feng Ding; Huifen Nie; Adrian Wendil Serohijos; Shantanu Sharma; Kyle C Wilcox; Shuangye Yin; Nikolay V Dokholyan
Protein folding: then and now.
Archives of biochemistry and biophysics 2008;469(1):4-19.
2007: Sagar D Khare; Nikolay V Dokholyan
Molecular mechanisms of polypeptide aggregation in human diseases.
Current protein & peptide science 2007;8(6):573-9.
2007: Shuangye Yin; Feng Ding; Nikolay V Dokholyan
Modeling backbone flexibility improves protein stability estimation.
Structure (London, England : 1993) 2007;15(12):1567-76.
2007: Shantanu Sharma; Peng Gong; Brenda Temple; Debadeep Bhattacharyya; Nikolay V Dokholyan; Stephen G Chaney
Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics.
Journal of molecular biology 2007;373(5):1123-40.
2007: A R Lam; Jose M Borreguero; Feng Ding; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Parallel folding pathways in the SH3 domain protein.
Journal of molecular biology 2007;373(5):1348-60.
2007: Yiwen Chen; Sharon L Campbell; Nikolay V Dokholyan
Deciphering protein dynamics from NMR data using explicit structure sampling and selection.
Biophysical journal 2007;93(7):2300-6.
2007: Sunjay Barton; Ron Jacak; Sagar D Khare; Feng Ding; Nikolay V Dokholyan
The length dependence of the polyQ-mediated protein aggregation.
The Journal of biological chemistry 2007;282(35):25487-92.
2007: Yiwen Chen; Feng Ding; Nikolay V Dokholyan
Fidelity of the protein structure reconstruction from inter-residue proximity constraints.
The journal of physical chemistry. B 2007;111(25):7432-8.
2007: Shuangye Yin; Feng Ding; Nikolay V Dokholyan
Eris: an automated estimator of protein stability.
Nature methods 2007;4(6):466-7.
2007: Charles H Davis; Huifen Nie; Nikolay V Dokholyan
Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes.
Physical review. E, Statistical, nonlinear, and soft matter physics 2007;75(5 Pt 1):051921.
2007: Shantanu Sharma; Feng Ding; Nikolay V Dokholyan
Multiscale modeling of nucleosome dynamics.
Biophysical journal 2007;92(5):1457-70.
2006: Adrian Wendil Serohijos; Yiwen Chen; Feng Ding; Timothy C Elston; Nikolay V Dokholyan
A structural model reveals energy transduction in dynein.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(49):18540-5.
2006: Evgeniy V Petrotchenko; Daniel A Pasek; Phillip Elms; Nikolay V Dokholyan; Gerhard Meissner; Christoph H Borchers
Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins.
Analytical chemistry 2006;78(23):7959-66.
2006: Sagar D Khare; Michael Caplow; Nikolay V Dokholyan
FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis.
Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis 2006;13(4):226-35.
2006: Shantanu Sharma; Feng Ding; Huifen Nie; Daniel Watson; Aditya Unnithan; Jameson Lopp; Diane Pozefsky; Nikolay V Dokholyan
iFold: a platform for interactive folding simulations of proteins.
Bioinformatics (Oxford, England) 2006;22(21):2693-4.
2006: Yiwen Chen; Nikolay V Dokholyan
Insights into allosteric control of vinculin function from its large scale conformational dynamics.
The Journal of biological chemistry 2006;281(39):29148-54.
2006: Yiwen Chen; Nikolay V Dokholyan
The coordinated evolution of yeast proteins is constrained by functional modularity.
Trends in genetics : TIG 2006;22(8):416-9.
2006: Feng Ding; Nikolay V Dokholyan
Emergence of protein fold families through rational design.
PLoS computational biology 2006;2(7):e85.
2006: Kerry Bloom; Shantanu Sharma; Nikolay V Dokholyan
The path of DNA in the kinetochore.
Current biology : CB 2006;16(8):R276-8.
2006: Sagar D Khare; Nikolay V Dokholyan
Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(9):3147-52.
2006: Vadim V Demidov; Nikolay V Dokholyan; Carlos Witte-Hoffmann; Poornima Chalasani; Hung-Wei Yiu; Feng Ding; Yong Yu; Charles R Cantor; Natalia E Broude
Fast complementation of split fluorescent protein triggered by DNA hybridization.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(7):2052-6.
2006: Nikolay V Dokholyan
Studies of folding and misfolding using simplified models.
Current opinion in structural biology 2006;16(1):79-85.
2006: Feng Ding; Kirk C Prutzman; Sharon L Campbell; Nikolay V Dokholyan
Topological determinants of protein domain swapping.
Structure (London, England : 1993) 2006;14(1):5-14.
2005: Feng Ding; Joshua J LaRocque; Nikolay V Dokholyan
Direct observation of protein folding, aggregation, and a prion-like conformational conversion.
The Journal of biological chemistry 2005;280(48):40235-40.
2005: Yiwen Chen; Nikolay V Dokholyan
A single disulfide bond differentiates aggregation pathways of beta2-microglobulin.
Journal of molecular biology 2005;354(2):473-82.
2005: Sagar D Khare; Kyle C Wilcox; Peng Gong; Nikolay V Dokholyan
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation.
Proteins 2005;61(3):617-32.
2005: Feng Ding; Nikolay V Dokholyan
Simple but predictive protein models.
Trends in biotechnology 2005;23(9):450-5.
2005: Sagar D Khare; Feng Ding; Kenneth N Gwanmesia; Nikolay V Dokholyan
Molecular origin of polyglutamine aggregation in neurodegenerative diseases.
PLoS computational biology 2005;1(3):230-5.
2005: Feng Ding; Weihua Guo; Nikolay V Dokholyan; Eugene I Shakhnovich; Joan-Emma Shea
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations.
Journal of molecular biology 2005;350(5):1035-50.
2005: Feng Ding; Ramesh K Jha; Nikolay V Dokholyan
Scaling behavior and structure of denatured proteins.
Structure (London, England : 1993) 2005;13(7):1047-54.
2005: Nikolay V Dokholyan
The architecture of the protein domain universe.
Gene 2005;347(2):199-206.
2005: Feng Ding; Sergey V Buldyrev; Nikolay V Dokholyan
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
Biophysical journal 2005;88(1):147-55.
2004: Richard D S Dixon; Yiwen Chen; Feng Ding; Sagar D Khare; Kirk C Prutzman; Michael D Schaller; Sharon L Campbell; Nikolay V Dokholyan
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate.
Structure (London, England : 1993) 2004;12(12):2161-71.
2004: Sagar D Khare; Michael Caplow; Nikolay V Dokholyan
The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(42):15094-9.
2004: Brigita Urbanc; Luis Cruz; Feng Ding; D Sammond; S Khare; Sergey V Buldyrev; H Eugene Stanley; Nikolay V Dokholyan
Molecular dynamics simulation of amyloid beta dimer formation.
Biophysical journal 2004;87(4):2310-21.
2004: Guido Tiana; Nikolay V Dokholyan; Ricardo A Broglia; Eugene I Shakhnovich
The evolution dynamics of model proteins.
The Journal of chemical physics 2004;121(5):2381-9.
2004: Jose M Borreguero; Feng Ding; Sergey V Buldyrev; H Eugene Stanley; Nikolay V Dokholyan
Multiple folding pathways of the SH3 domain.
Biophysical journal 2004;87(1):521-33.
2004: Shouyong Peng; Feng Ding; Brigita Urbanc; Sergey V Buldyrev; Luis Cruz; H Eugene Stanley; Nikolay V Dokholyan
Discrete molecular dynamics simulations of peptide aggregation.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;69(4 Pt 1):041908.
2004: Jainab Khatun; Sagar D Khare; Nikolay V Dokholyan
Can contact potentials reliably predict stability of proteins?
Journal of molecular biology 2004;336(5):1223-38.
2004: Guido Tiana; Borya Shakhnovich; Nikolay V Dokholyan; Eugene I Shakhnovich
Imprint of evolution on protein structures.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):2846-51.
2004: Nikolay V Dokholyan
What is the protein design alphabet?
Proteins 2004;54(4):622-8.
2003: Sagar D Khare; Feng Ding; Nikolay V Dokholyan
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis.
Journal of molecular biology 2003;334(3):515-25.
2003: Eric J Deeds; Nikolay V Dokholyan; Eugene I Shakhnovich
Protein evolution within a structural space.
Biophysical journal 2003;85(5):2962-72.
2003: Feng Ding; Jose M Borreguero; Sergey V Buldyrey; H Eugene Stanley; Nikolay V Dokholyan
Mechanism for the alpha-helix to beta-hairpin transition.
Proteins 2003;53(2):220-8.
2003: Jimin Pei; Nikolay V Dokholyan; Eugene I Shakhnovich; Nick V Grishin
Using protein design for homology detection and active site searches.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11361-6.
2003: Miriam Marqués; Jose M Borreguero; H Eugene Stanley; Nikolay V Dokholyan
Possible mechanism for cold denaturation of proteins at high pressure.
Physical review letters 2003;91(13):138103.
2003: Eduardo López; Sergey V Buldyrev; Nikolay V Dokholyan; Leo Goldmakher; Shlomo Havlin; Peter R King; H Eugene Stanley
Postbreakthrough behavior in flow through porous media.
Physical review. E, Statistical, nonlinear, and soft matter physics 2003;67(5 Pt 2):056314.
2003: Borya Shakhnovich; Nikolay V Dokholyan; Charles DeLisi; Eugene I Shakhnovich
Functional fingerprints of folds: evidence for correlated structure-function evolution.
Journal of molecular biology 2003;326(1):1-9.
2003: Nikolay V Dokholyan; Jose M Borreguero; Sergey V Buldyrev; Feng Ding; H Eugene Stanley; Eugene I Shakhnovich
Identifying importance of amino acids for protein folding from crystal structures.
Methods in enzymology 2003;374():616-38.
2002: Feng Ding; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism.
Journal of molecular biology 2002;324(4):851-7.
2002: Feng Ding; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Direct molecular dynamics observation of protein folding transition state ensemble.
Biophysical journal 2002;83(6):3525-32.
2002: Nikolay V Dokholyan; Borya Shakhnovich; Eugene I Shakhnovich
Expanding protein universe and its origin from the biological Big Bang.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(22):14132-6.
2002: Nikolay V Dokholyan; Lewyn Li; Feng Ding; Eugene I Shakhnovich
Topological determinants of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(13):8637-41.
2002: M Vendruscolo; Nikolay V Dokholyan; E Paci; M Karplus
Small-world view of the amino acids that play a key role in protein folding.
Physical review. E, Statistical, nonlinear, and soft matter physics 2002;65(6 Pt 1):061910.
2002: Jose M Borreguero; Nikolay V Dokholyan; Sergey V Buldyrev; Eugene I Shakhnovich; H Eugene Stanley
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.
Journal of molecular biology 2002;318(3):863-76.
2002: Nikolay V Dokholyan; Estelle Pitard; Sergey V Buldyrev; H Eugene Stanley
Glassy behavior of a homopolymer from molecular dynamics simulations.
Physical review. E, Statistical, nonlinear, and soft matter physics 2002;65(3 Pt 1):030801.
2001: Nikolay V Dokholyan; Eugene I Shakhnovich
Understanding hierarchical protein evolution from first principles.
Journal of molecular biology 2001;312(1):289-307.
2001: Antonio Scala; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley
Thermodynamically important contacts in folding of model proteins.
Physical review. E, Statistical, nonlinear, and soft matter physics 2001;63(3 Pt 1):032901.
2000: Nikolay V Dokholyan; S V Buldyrev; H Eugene Stanley; E I Shakhnovich
Identifying the protein folding nucleus using molecular dynamics.
Journal of molecular biology 2000;296(5):1183-8.
2000: Nikolay V Dokholyan; S V Buldyrev; S Havlin; H Eugene Stanley
Distributions of dimeric tandem repeats in non-coding and coding DNA sequences.
Journal of theoretical biology 2000;202(4):273-82.
1999: Y Lee; José S Andrade; Sergey V Buldyrev; Nikolay V Dokholyan; Shlomo Havlin; P R King; G Paul; H Eugene Stanley
Traveling time and traveling length in critical percolation clusters.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 1999;60(3):3425-8.
1999: R H Stanley; Nikolay V Dokholyan; Sergey V Buldyrev; Shlomo Havlin; H Eugene Stanley
Clustering of identical oligomers in coding and noncoding DNA sequences.
Journal of biomolecular structure & dynamics 1999;17(1):79-87.
1998: Nikolay V Dokholyan; S V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Discrete molecular dynamics studies of the folding of a protein-like model.
Folding & design 1998;3(6):577-87.