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2012 Feature Articles

2011 Feature Articles

SYNTHETIC BIOLOGY AND CHEMISTRY

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P.
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Simplification of the Genetic Code: Restricted Diversity of Genetically Encoded Amino Acids
Kawahara-Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, Asami S, Matsuda T, Ishitani R, Dohmae N, Yokoyama S, Kigawa T, Nureki O, Kiga D.
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Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation
Kashida S, Inoue T, Saito H.
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Modular control of multiple pathways using engineered orthogonal T7 polymerases
Temme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA.
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Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases
Daboussi F, Zaslavskiy M, Poirot L, Loperfido M, Gouble A, Guyot V, Leduc S, Galetto R, Grizot S, Oficjalska D, Perez C, Delacôte F, Dupuy A, Chion-Sotinel I, Le Clerre D, Lebuhotel C, Danos O, Lemaire F, Oussedik K, Cédrone F, Epinat JC, Smith J, Dickson
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Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences
Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA.
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Transgene regulation in plants by alternative splicing of a suicide exon
Hickey SF, Sridhar M, Westermann AJ, Qin Q, Vijayendra P, Liou G, Hammond MC.
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Configuring robust DNA strand displacement reactions for in situ molecular analyses
Dzifa Y. Duose, Ryan M. Schweller, Jan Zimak, Arthur R. Rogers, Walter N. Hittelman, and Michael R. Diehl
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COMPUTATIONAL BIOLOGY

A complex network framework for unbiased statistical analyses of DNA-DNA contact maps
Kruse K, Sewitz S, Babu MM.
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MuMoD: A Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data
Narlikar L.
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Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels
Hlevnjak M, Polyansky AA, Zagrovic B.
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Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde
Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D.
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Unrecognized sequence homologies may confound genome-wide association studies
Galichon P, Mesnard L, Hertig A, Stengel B, Rondeau E.
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Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
Do-Nyun Kim, Fabian Kilchherr, Hendrik Dietz, and Mark Bathe
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GENE REGULATION, CHROMATIN AND EPIGENETICS

Promoter cross-talk via a shared enhancer explains paternally biased expression of Nctc1 at the Igf2/H19/Nctc1 imprinted locus
Eun B, Sampley ML, Good AL, Gebert CM, Pfeifer K.
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Ablation of PRMT6 reveals a role as a negative transcriptional regulator of the p53 tumor suppressor
Neault M, Mallette FA, Vogel G, Michaud-Levesque J, Richard S.
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The arginine methyltransferase PRMT6 regulates cell proliferation and senescence through transcriptional repression of tumor suppressor genes
Stein C, Riedl S, Rüthnick D, Nötzold RR, Bauer UM.
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Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes
Liu HW, Zhang J, Heine GF, Arora M, Gulcin Ozer H, Onti-Srinivasan R, Huang K, Parvin JD.
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Promoters Active in Interphase are Bookmarked during Mitosis by Ubiquitination
Arora M, Zhang J, Heine GF, Ozer G, Liu HW, Huang K, Parvin JD.
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MyoD regulates p57kip2 expression by interacting with a distant cis-element and modifying a higher order chromatin structure
Busanello A, Battistelli C, Carbone M, Mostocotto C, Maione R.
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Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island
Zhang Y, Shu J, Si J, Shen L, Estecio MR, Issa JP.
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Evidence that RNA polymerase II and not TFIIB is responsible for the difference in transcription initiation patterns between Saccharomyces cerevisiae and Schizosaccharomyces pombe
Chen Yang and Alfred S. Ponticelli
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Drosophila melanogaster linker histone dH1 is required for transposon silencing and to preserve genome integrity
Vujatovic O, Zaragoza K, Vaquero A, Reina O, Bernués J, Azorín F.
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The HTLV-1-encoded protein HBZ directly inhibits the acetyl transferase activity of p300/CBP
Wurm T, Wright DG, Polakowski N, Mesnard JM, Lemasson I.
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Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site
Senigl F, Auxt M, Hejnar J.
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Zinc induced Dnmt1 expression involves antagonism between MTF-1 and nuclear receptor SHP
Zhang Y, Andrews GK, Wang L.
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Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5
Gary Loughran, Matthew S. Sachs, John F. Atkins, and Ivaylo P. Ivanov
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Gli2 and MEF2C activate each other’s expression and function synergistically during cardiomyogenesis in vitro
Anastassia Voronova, Ashraf Al Madhoun, Anna Fischer, Michael Shelton, Christina Karamboulas, and Ilona Sylvia Skerjanc
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Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
Johannes M. Freudenberg, Swati Ghosh, Brad L. Lackford, Sailu Yellaboina, Xiaofeng Zheng, Ruifang Li, Suresh Cuddapah, Paul A. Wade, Guang Hu, and Raja Jothi
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Yin Yang 1 extends the Myc-related Transcription Factors Network in Embryonic Stem Cells
Pietro Vella, Iros Barozzi, Alessandro Cuomo, Tiziana Bonaldi, and Diego Pasini
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GENOME INTEGRITY, REPAIR AND REPLICATION

A SUMO-interacting motif activates budding yeast ubiquitin ligase Rad18 towards SUMO-modified PCNA
Parker JL, Ulrich HD.
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DOT1A-dependent H3K76 methylation is required for replication regulation in Trypanosoma brucei
Gassen A, Brechtefeld D, Schandry N, Arteaga-Salas JM, Israel L, Imhof A, Janzen CJ.
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A small RNA response at DNA ends in Drosophila
Michalik KM, Böttcher R, Förstemann K
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Cell cycle-dependent regulation of the nuclease activity of Mus81-Eme1/Mms4
Gallo-Fernández M, Saugar I, Ortiz-Bazán MA, Vázquez MV, Tercero JA.
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Quantitative proteomics profiling of the poly(ADP-ribose)-related response to genotoxic stress
Gagné JP, Pic E, Isabelle M, Krietsch J, Ethier C, Paquet E, Kelly I, Boutin M, Moon KM, Foster LJ, Poirier GG.
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Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain
Jinping Liu, Shukun Luo, Hongchang Zhao, Ji Liao, Jing Li, Chunying Yang, Bo Xu, David F. Stern, Xingzhi Xu, and Keqiong Ye
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The molecular basis of ATM-dependent dimerization of the Mdc1 DNA-damage checkpoint mediator
Stephanie Jungmichel, Julie A. Clapperton, Janette Lloyd, Flurina J. Hari, Christoph Spycher, Lucijana Pavic, Jiejin Li, Lesley F. Haire, Mario Bonalli, Dorthe H. Larsen, Claudia Lukas, Jiri Lukas, Derek MacMillan, Michael L. Nielsen, Manuel Stucki, and Stephen J. Smerdon
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GENOMICS

The Methylomes of Six Bacteria
Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ.
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Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution
Saini V, Raghuvanshi S, Khurana JP, Ahmed N, Hasnain SE, Tyagi AK.
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Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation
de Klerk E, Venema A, Anvar SY, Goeman JJ, Hu O, den Dunnen JT, van der Maarel SM, Raz V, 't Hoen PA
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Cell type-specific genomics of Drosophila neurons
Henry GL, Davis FP, Picard S, Eddy SR
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Genome-wide occupancy links Hoxa2 to Wnt-beta-catenin signaling in mouse embryonic development
Ian J. Donaldson, Shilu Amin, James J. Hensman, Eva Kutejova, Magnus Rattray, Neil Lawrence, Andrew Hayes, Christopher M. Ward, and Nicoletta Bobola
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MOLECULAR BIOLOGY

Circular retrotransposition products generated by a LINE retrotransposon
Han JS, Shao S.
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Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer
Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Qian H, Strahl BD, Blancafort P.
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A novel phage-encoded transcription antiterminator acts by suppressing pausing by bacterial RNA polymerase
Zhanna Berdygulova, Daria Esyunina, Nataliya Miropolskaya, Damir Mukhamedyarov, Konstantin Kuznedelov, Bryce E. Nickels, Konstantin Severinov, Andrey Kulbachinskiy, and Leonid Minakhin
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P1 AND P2 PROTEIN HETERODIMER BINDING TO THE P0 PROTEIN OF Saccharomyces cerevisiae IS RELATIVELY NON-SPECIFIC AND A SOURCE OF RIBOSOMAL HETEROGENEITY
David Cárdenas, Jesús Revuelta-Cervantes, Antonio Jiménez-Díaz, Hendricka Camargo, Miguel Remacha, and Juan P. G. Ballesta
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DNA robustly stimulates FANCD2 monoubiquitylation in the complex with FANCI
Koichi Sato, Kazue Toda, Masamichi Ishiai, Minoru Takata, and Hitoshi Kurumizaka
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NUCLEIC ACID ENZYMES

A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase – extensive moonlighting in mitochondrial tRNA biogenesis
Vilardo E, Nachbagauer C, Buzet A, Taschner A, Holzmann J, Rossmanith W.
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The sequential 2′,3′-cyclic phosphodiesterase and 3′-phosphate/5′-OH ligation steps of the RtcB RNA splicing pathway are GTP-dependent
Chakravarty AK, Shuman S.
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Rational engineering of sequence specificity in R.MwoI restriction endonuclease
Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM.
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Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I
Markiewicz RP, Vrtis KB, Rueda D, Romano LJ.
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Mechanism of strand displacement synthesis by DNA replicative polymerases
Manosas M, Spiering MM, Ding F, Bensimon D, Allemand JF, Benkovic SJ, Croquette V.
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Collaborative coupling between polymerase and helicase for leading-strand synthesis
Manosas M, Spiering MM, Ding F, Croquette V, Benkovic SJ.
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DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics
Laurens N, Rusling DA, Pernstich C, Brouwer I, Halford SE, Wuite GJ.
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DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations
Rusling DA, Laurens N, Pernstich C, Wuite GJ, Halford SE.
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Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences
Bao Ton-Hoang, Patricia Siguier, Yves Quentin, Séverine Onillon, Brigitte Marty, Gwennaele Fichant, and Mick Chandler
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RNA

The mammalian TRIM-NHL protein TRIM71/ LIN-41 is a repressor of mRNA function
Loedige I, Gaidatzis D, Sack R, Meister G, Filipowicz W.
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The transition in spliceosome assembly from complex E to complex A purges surplus U1 snRNPs from alternative splice sites
Mark J. Hodson, Andrew J. Hudson, Dmitry Cherny, and Ian C. Eperon
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Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation
Holub P, Lalakova J, Cerna H, Pasulka J, Sarazova M, Hrazdilova K, Arce MS, Hobor F, Stefl R, Vanacova S.
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Aberrant growth and lethality of Arabidopsis deficient in nonsense mediated RNA decay factors is caused by autoimmune-like response
Riehs-Kearnan N, Gloggnitzer J, Dekrout B, Jonak C, Riha K.
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Widespread occurrence of 5-methylcytosine in human coding and noncoding RNA
Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T.
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Utp23p is required for dissociation of snR30 small nucleolar RNP from pre-ribosomal particles
Coralie Hoareau-Aveilla, Eléonore Fayet-Lebaron, Beáta E. Jády, Anthony K. Henras, and Tamás Kiss
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BC1-FMRP interaction is modulated by 2’-O Methylation: RNA binding activity of the Tudor domain and translational regulation at synapses
Caroline Lacoux, Daniele Di Marino, Pietro Pilo Boyl, Francesca Zalfa, Bing Yan, Maria Teresa Ciotti, Mattia Falconi, Henning Urlaub, Tilmann Achsel, Annie Mougin, Michèle Caizergues-Ferrer, and Claudia Bagni
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mRNA Knockdown by Single Strand RNA is Improved by Chemical Modifications
Henry J. Haringsma, Jenny J. Li, Ferdie Soriano, Denise M. Kenski, W. Michael Flanagan, and Aarron T. Willingham
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Biogenesis of mammalian microRNAs by a non-canonical processing pathway
Mallory A. Havens, Ashley A. Reich, Dominik M. Duelli, and Michelle L. Hastings
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STRUCTURAL BIOLOGY

Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition
Zhang Y, Madl T, Bagdiul I, Kern T, Kang HS, Zou P, Mäusbacher N, Sieber SA, Krämer A, Sattler M.
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The structural basis for the interaction between CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex
Petit AP, Wohlbold L, Bawankar P, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O.
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The processing of Repetitive Extragenic Palindromes: The structure of a REP bound to its associated nuclease
Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F.
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Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme
Benjdia A, Heil K, Barends TR, Carell T, Schlichting I.
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Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex
Kobayashi K, Saito K, Ishitani R, Ito K, Nureki O
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METHODS ONLINE

Fluorescent Signatures for Variable DNA Sequences
Rice JE, Reis AH Jr, Rice LM, Carver-Brown RK, Wangh LJ.
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Compression of next-generation sequencing reads aided by highly efficient de novo assembly
Jones DC, Ruzzo WL, Peng X, Katze MG.
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A benchmark for chromatin binding measurements in live cells
Mazza D, Abernathy A, Golob N, Morisaki T, McNally JG.
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i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules
Herrmann C, Van de Sande B, Potier D, Aerts S.
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Primer3--new capabilities and interfaces
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG.
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Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers
Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM.
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Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker
John T. Heap, Muhammad Ehsaan, Clare M. Cooksley, Yen-Kuan Ng, Stephen T. Cartman, Klaus Winzer, and Nigel P. Minton
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SURVEY AND SUMMARY

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily
Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K.
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Prospects and limitations of full-text index structures in genome analysis
Vyverman M, De Baets B, Fack V, Dawyndt P.
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Homologous recombination and its regulation
Krejci L, Altmannova V, Spirek M, Zhao X.
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DATABASE SPECIAL ISSUE

Polbase : a repository of biochemical, genetic, and structural information about DNA polymerases
Langhorst BW, Jack WE, Reha-Krantz L, Nichols NM.
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ALFRED: an allele frequency resource for research and teaching
Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK.
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SMART 7: Recent updates to the protein domain annotation resource
Letunic I, Doerks T, Bork P.
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Gene Expression Atlas update – a value-added database of microarray and sequencing-based functional genomics experiments
Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N et al.
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Ensembl Genomes: An Integrative Resource for Genome-Scale Data from non-Vertebrate Species
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G et al.
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WormBase 2012: More Genomes, More Data, New Website
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R et al.
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The Mouse Genome Database (MGD): Comprehensive Resource for Genetics and Genomics of the Laboratory Mouse
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; the Mouse Genome Database Group.
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Pocketome: an encyclopedia of small-molecule binding sites in 4D
Kufareva I, Ilatovskiy AV, Abagyan R.
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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
Rawlings ND, Barrett AJ, Bateman A.
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doRiNA: a database of RNA interactions in post-transcriptional regulation
Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C.
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IMG/M: the integrated metagenome data management and comparative analysis system
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M et al.
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PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update
Wang X, Spandidos A, Wang H, Seed B.
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InterPro in 2011: New developments in the family and domain prediction database
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al.
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eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T et al.
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Reorganizing the protein space at the Universal Protein Resource (UniProt)
The UniProt Consortium
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UniPathway: a resource for the exploration and annotation of metabolic pathways.
Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A.
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Mouse Phenome Database (MPD)
Maddatu TP, Grubb SC, Bult CJ, Bogue MA.
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Comparative interactomics with Funcoup 2.0
Alexeyenko A, Schmitt T, Tjärnberg A, Guala D, Frings O, Sonnhammer EL.
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ELM – the database of eukaryotic linear motifs.
Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A et al.
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The Genome Portal of the Department of Energy Joint Genome Institute
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA et al.
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The IntAct molecular interaction database in 2012
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U et al.
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The UniProt-GO Annotation Database in 2011
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M et al.
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The Pfam Protein Families Database
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al.
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The DARC site: a Database of Aligned Ribosomal Complexes
Jarasch A, Dziuk P, Becker T, Armache JP, Hauser A, Wilson DN, Beckmann R.
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Tarbase 6.0: Capturing the Exponential Growth of miRNA Targets with Experimental Support
Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, and Hatzigeorgiou AG.
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The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M et al.
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PubChem’s BioAssay Database
Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA et al.
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ScerTF: A comprehensive database of benchmarked position weight matrices for Saccharomyces species
Spivak AT, Stormo GD.
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WEB SERVER SPECIAL ISSUE

CSA: comprehensive comparison of pairwise protein structure alignments
Wohlers I, Malod-Dognin N, Andonov R, Klau GW.
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IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.
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TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage
Brandt BW, Bonder MJ, Huse SM, Zaura E.
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PepSite: prediction of peptide-binding sites from protein surfaces
Trabuco LG, Lise S, Petsalaki E, Russell RB
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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
Anandakrishnan R, Aguilar B, Onufriev AV.
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Monte Carlo simulations of peptide-membrane interactions with the MCPep web server
Gofman Y, Haliloglu T, Ben-Tal N.
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