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PocketPicker: analysis of ligand binding-sites with shape descriptors
Martin Weisel, Ewgenij Proschak, Gisbert Schneider
Chem Cent J. 2007; 1: 7. Published online 2007 March 13. doi: 10.1186/1752-153X-1-7
PMCID:
PMC1994066
Abstract Full Text PDF–2.1M Supplementary Material

Is Cited by the Following 28 Articles in this Archive:

Distinct Roles of Secreted HtrA Proteases from Gram-negative Pathogens in Cleaving the Junctional Protein and Tumor Suppressor E-cadherin
Benjamin Hoy, Tim Geppert, Manja Boehm, Felix Reisen, Patrick Plattner, Gabriele Gadermaier, Norbert Sewald, Fatima Ferreira, Peter Briza, Gisbert Schneider, Steffen Backert, Silja Wessler
J Biol Chem. 2012 March 23; 287(13): 10115–10120. Published online 2012 February 15. doi: 10.1074/jbc.C111.333419
PMCID:
PMC3323053
Free in PMC on 2013/03/23
Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
Tianyun Liu, Russ B. Altman
PLoS Comput Biol. 2011 December; 7(12): e1002326. Published online 2011 December 29. doi: 10.1371/journal.pcbi.1002326
PMCID:
PMC3248393
Abstract Full Text PDF–2.9M Supplementary Material
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu
BMC Bioinformatics. 2011; 12(Suppl 14): S9. Published online 2011 December 14. doi: 10.1186/1471-2105-12-S14-S9
PMCID:
PMC3287474
Abstract Full Text PDF–547K
Prediction of functionally important residues in globular proteins from unusual central distances of amino acids
Marek Kochańczyk
BMC Struct Biol. 2011; 11: 34. Published online 2011 September 18. doi: 10.1186/1472-6807-11-34
PMCID:
PMC3188475
Abstract Full Text PDF–789K Supplementary Material
Structure-based drug design of a new chemical class of small molecules active against influenza A nucleoprotein in vitro and in vivo
Peter Fedichev, Roman Timakhov, Tim Pyrkov, Evgeny Getmantsev, Andrey Vinnik
PLoS Curr. 2011 August 7; 3: RRN1253. doi: 10.1371/currents.RRN1253
PMCID:
PMC3153361
Abstract Full Text
Small-molecule inhibitor binding to an N-acyl-homoserine lactone synthase
Jiwoung Chung, Eunhye Goo, Sangheon Yu, Okhee Choi, Jeehyun Lee, Jinwoo Kim, Hongsup Kim, Jun Igarashi, Hiroaki Suga, Jae Sun Moon, Ingyu Hwang, Sangkee Rhee
Proc Natl Acad Sci U S A. 2011 July 19; 108(29): 12089–12094. Published online 2011 July 5. doi: 10.1073/pnas.1103165108
PMCID:
PMC3141922
Abstract Full Text PDF–827K Supplementary Material
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information
Rong Liu, Jianjun Hu
BMC Bioinformatics. 2011; 12: 207. Published online 2011 May 26. doi: 10.1186/1471-2105-12-207
PMCID:
PMC3124436
Abstract Full Text PDF–4.7M Supplementary Material
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
Kuan Pern Tan, Raghavan Varadarajan, M. S. Madhusudhan
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W242–W248. Published online 2011 May 14. doi: 10.1093/nar/gkr356
PMCID:
PMC3125764
Abstract Full Text PDF–3.4M
Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures
Dario Ghersi, Roberto Sanchez
J Struct Funct Genomics. Author manuscript; available in PMC 2012 July 1.
Published in final edited form as: J Struct Funct Genomics. 2011 July; 12(2): 109–117. Published online 2011 May 3. doi: 10.1007/s10969-011-9110-6
PMCID:
PMC3127736
Free in PMC on 2012/07/01
Recent advances in B-cell epitope prediction methods
Yasser EL-Manzalawy, Vasant Honavar
Immunome Res. 2010; 6(Suppl 2): S2. Published online 2010 November 3. doi: 10.1186/1745-7580-6-S2-S2
PMCID:
PMC2981878
Abstract Full Text PDF–279K
Relating the shape of protein binding sites to binding affinity profiles: is there an association?
Zoltán Simon, Margit Vigh-Smeller, Ágnes Peragovics, Gábor Csukly, Gergely Zahoránszky-Kőhalmi, Anna Á Rauscher, Balázs Jelinek, Péter Hári, István Bitter, András Málnási-Csizmadia, Pál Czobor
BMC Struct Biol. 2010; 10: 32. Published online 2010 October 5. doi: 10.1186/1472-6807-10-32
PMCID:
PMC2972294
Abstract Full Text PDF–1.4M
Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
Enrico De Franchi, Claire Schalon, Mirko Messa, Franco Onofri, Fabio Benfenati, Didier Rognan
PLoS One. 2010; 5(8): e12214. Published online 2010 August 16. doi: 10.1371/journal.pone.0012214
Correction in:
PLoS One. 2010; 5(10): 10.1371/annotation/95078306-dc3b-4441-b2b1-dd986b734570.
PMCID:
PMC2922380
Abstract Full Text PDF–598K Supplementary Material Correction
PoxA, YjeK and Elongation Factor P Coordinately Modulate Virulence and Drug Resistance in Salmonella enterica
William Wiley Navarre, Shicong Zou, Hervé Roy, Jinglin Lucy Xie, Alexei Savchenko, Alexander Singer, Elena Edvokimova, Lynne R. Prost, Runjun Kumar, Michael Ibba, Ferric C. Fang
Mol Cell. Author manuscript; available in PMC 2011 July 30.
Published in final edited form as: Mol Cell. 2010 July 30; 39(2): 209–221. doi: 10.1016/j.molcel.2010.06.021
PMCID:
PMC2913146
Abstract Full Text PDF–1.1M Supplementary Material
Mapping the Druggable Allosteric Space of G-Protein Coupled Receptors: a Fragment-Based Molecular Dynamics Approach
Anthony Ivetac, J. Andrew McCammon
Chem Biol Drug Des. Author manuscript; available in PMC 2011 September 1.
Published in final edited form as: Chem Biol Drug Des. 2010 September 1; 76(3): 201–217. Published online 2010 July 5. doi: 10.1111/j.1747-0285.2010.01012.x
PMCID:
PMC2918726
Abstract Full Text PDF–3.5M Supplementary Material
Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors
Rayan Chikhi, Lee Sael, Daisuke Kihara
Proteins. Author manuscript; available in PMC 2011 July 1.
Published in final edited form as: Proteins. 2010 July; 78(9): 2007–2028. doi: 10.1002/prot.22715
PMCID:
PMC3009464
Abstract Full Text PDF–1.8M
Boron Toxicity Tolerance in Barley through Reduced Expression of the Multifunctional Aquaporin HvNIP2;1
Thorsten Schnurbusch, Julie Hayes, Maria Hrmova, Ute Baumann, Sunita A. Ramesh, Stephen D. Tyerman, Peter Langridge, Tim Sutton
Plant Physiol. 2010 August; 153(4): 1706–1715. Published online 2010 June 25. doi: 10.1104/pp.110.158832
PMCID:
PMC2923888
Abstract Full Text PDF–729K Supplementary Material
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble
Edon Sung, Sangsoo Kim, Whanchul Shin
BMC Bioinformatics. 2010; 11: 256. Published online 2010 May 18. doi: 10.1186/1471-2105-11-256
PMCID:
PMC3098062
Abstract Full Text PDF–2.5M Supplementary Material
Structure of the d-alanylgriseoluteic acid biosynthetic protein EhpF, an atypical member of the ANL superfamily of adenylating enzymes
Asim K. Bera, Vesna Atanasova, Swarna Gamage, Howard Robinson, James F. Parsons
Acta Crystallogr D Biol Crystallogr. 2010 June 1; 66(Pt 6): 664–672. Published online 2010 May 15. doi: 10.1107/S0907444910008425
PMCID:
PMC2879354
Abstract Full Text PDF–1.9M Supplementary Material
Where are the boundaries? Automated pocket detection for druggability studies
Andrea Volkamer, T Grombacher, Matthias Rarey
J Cheminform. 2010; 2(Suppl 1): P11. Published online 2010 May 4. doi: 10.1186/1758-2946-2-S1-P11
PMCID:
PMC2867143
Full Text PDF–149K
Mapping of Ligand-Binding Cavities in Proteins
C. David Andersson, Brian Y. Chen, Anna Linusson
Proteins. Author manuscript; available in PMC 2011 May 1.
Published in final edited form as: Proteins. 2010 May 1; 78(6): 1408–1422. doi: 10.1002/prot.22655
Correction in:
Proteins. 2011 April; 79(4): 1363.
PMCID:
PMC2957484
Abstract Full Text PDF–3.0M Supplementary Material Correction
A Novel and Efficient Tool for Locating and Characterizing Protein Cavities and Binding Sites
Ashutosh Tripathi, Glen E. Kellogg
Proteins. Author manuscript; available in PMC 2011 March 1.
Published in final edited form as: Proteins. 2010 March; 78(4): 825–842. doi: 10.1002/prot.22608
PMCID:
PMC2811767
Abstract Full Text PDF–4.0M
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues
Shirley Wu, Tianyun Liu, Russ B Altman
BMC Struct Biol. 2010; 10: 4. Published online 2010 February 2. doi: 10.1186/1472-6807-10-4
PMCID:
PMC2833161
Abstract Full Text PDF–2.8M Supplementary Material
fPOP: footprinting functional pockets of proteins by comparative spatial patterns
Yan Yuan Tseng, Z. Jeffrey Chen, Wen-Hsiung Li
Nucleic Acids Res. 2010 January; 38(Database issue): D288–D295. Published online 2010 January. doi: 10.1093/nar/gkp900
PMCID:
PMC2808891
Abstract Full Text PDF–5.5M
Crystal Structure and Functional Analysis of the Extradiol Dioxygenase LapB from a Long-chain Alkylphenol Degradation Pathway in Pseudomonas
Jang-Hee Cho, Du-Kyo Jung, Kyoung Lee, Sangkee Rhee
J Biol Chem. 2009 December 4; 284(49): 34321–34330. Published online 2009 October 14. doi: 10.1074/jbc.M109.031054
PMCID:
PMC2797200
Abstract Full Text
Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation
Benjamin Stauch, Henning Hofmann, Mario Perković, Martin Weisel, Ferdinand Kopietz, Klaus Cichutek, Carsten Münk, Gisbert Schneider
Proc Natl Acad Sci U S A. 2009 July 21; 106(29): 12079–12084. Published online 2009 July 6. doi: 10.1073/pnas.0900979106
PMCID:
PMC2715496
Abstract Full Text PDF–1.2M Supplementary Material
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
Izhar Wallach, Ryan H. Lilien
Bioinformatics. 2009 June 15; 25(12): i296–i304. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp204
PMCID:
PMC2687958
Abstract Full Text PDF–480K
VASCo: computation and visualization of annotated protein surface contacts
Georg Steinkellner, Robert Rader, Gerhard G Thallinger, Christoph Kratky, Karl Gruber
BMC Bioinformatics. 2009; 10: 32. Published online 2009 January 24. doi: 10.1186/1471-2105-10-32
PMCID:
PMC2649047
Abstract Full Text PDF–4.7M Supplementary Material
Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments
Olivier Sperandio, Maria A Miteva, Kenneth Segers, Gerry A. F Nicolaes, Bruno O Villoutreix
Open Biochem J. 2008; 2: 29–37. Published online 2008 March 10. doi: 10.2174/1874091X00802010029
PMCID:
PMC2570552
Abstract Full Text PDF–349K
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