Sandor Vajda

Sandor Vajda

UNVERIFIED PROFILE

Are you Sandor Vajda?   Register this Author

Register author
Sandor Vajda

Sandor Vajda

Publications by authors named "Sandor Vajda"

Are you Sandor Vajda?   Register this Author

100Publications

1586Reads

18Profile Views

Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment.

Authors:
Marc F Lensink Guillaume Brysbaert Nurul Nadzirin Sameer Velankar Raphaël A G Chaleil Tereza Gerguri Paul A Bates Elodie Laine Alessandra Carbone Sergei Grudinin Ren Kong Ran-Ran Liu Xi-Ming Xu Hang Shi Shan Chang Miriam Eisenstein Agnieszka Karczynska Cezary Czaplewski Emilia Lubecka Agnieszka Lipska Paweł Krupa Magdalena Mozolewska Łukasz Golon Sergey Samsonov Adam Liwo Silvia Crivelli Guillaume Pagès Mikhail Karasikov Maria Kadukova Yumeng Yan Sheng-You Huang Mireia Rosell Luis Angel Rodríguez-Lumbreras Miguel Romero-Durana Lucía Díaz-Bueno Juan Fernandez-Recio Charles Christoffer Genki Terashi Woong-Hee Shin Tunde Aderinwale Sai Raghavendra Maddhuri Venkata Subraman Daisuke Kihara Dima Kozakov Sandor Vajda Kathyn Porter Dzmitry Padhorny Israel Desta Dmitri Beglov Mikhail Ignatov Sergey Kotelnikov Iain H Moal David W Ritchie Isaure Chauvot de Beauchêne Bernard Maigret Marie-Dominique Devignes Maria Elisa Ruiz Echartea Didier Barradas-Bautista Zhen Cao Luigi Cavallo Romina Oliva Yue Cao Yang Shen Minkyung Baek Taeyong Park Hyeonuk Woo Chaok Seok Merav Braitbard Lirane Bitton Dina Scheidman-Duhovny Justas DapkŪnas Kliment Olechnovič Česlovas Venclovas Petras J Kundrotas Saveliy Belkin Devlina Chakravarty Varsha D Badal Ilya A Vakser Thom Vreven Sweta Vangaveti Tyler Borrman Zhiping Weng Johnathan D Guest Ragul Gowthaman Brian G Pierce Xianjin Xu Rui Duan Liming Qiu Jie Hou Benjamin Ryan Merideth Zhiwei Ma Jianlin Cheng Xiaoqin Zou Panos I Koukos Jorge Roel-Touris Francesco Ambrosetti Cunliang Geng Jörg Schaarschmidt Mikael E Trellet Adrien S J Melquiond Li Xue Brian Jiménez-García Charlotte W van Noort Rodrigo V Honorato Alexandre M J J Bonvin Shoshana J Wodak

Proteins 2019 Oct 14. Epub 2019 Oct 14.

VIB Structural Biology Research Center, VUB, Pleinlaan 2, B-1050, Brussels, Belgium.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.25838DOI Listing
October 2019

Amidino-Rocaglates: A Potent Class of eIF4A Inhibitors.

Cell Chem Biol 2019 Sep 10. Epub 2019 Sep 10.

Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Oncology, McGill University, Montreal, Canada; Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chembiol.2019.08.008DOI Listing
September 2019

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.

J Med Chem 2019 Jul 5;62(14):6512-6524. Epub 2019 Jul 5.

Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology , University of California , 1700 Fourth Street , San Francisco , California 9415 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jmedchem.9b00089DOI Listing
July 2019

Mapping global protein contacts.

Science 2019 07;365(6449):120-121

Departments of Biomedical Engineering, Biochemistry, and Biology, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aay1440DOI Listing
July 2019

Why Some Targets Benefit from beyond Rule of Five Drugs.

J Med Chem 2019 Jun 26. Epub 2019 Jun 26.

Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jmedchem.8b01732DOI Listing
June 2019

What method to use for protein-protein docking?

Curr Opin Struct Biol 2019 Apr 1;55:1-7. Epub 2019 Feb 1.

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Chemistry, Boston University, Boston, MA 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S0959440X183006
Publisher Site
http://dx.doi.org/10.1016/j.sbi.2018.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6669123PMC
April 2019

Analysis of tractable allosteric sites in G protein-coupled receptors.

Sci Rep 2019 Apr 16;9(1):6180. Epub 2019 Apr 16.

Medicinal Chemistry Research Group, Research Center for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-42618-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467999PMC
April 2019

Structure-based druggability assessment of anti-virulence targets from Pseudomonas aeruginosa.

Curr Protein Pept Sci 2019 Apr 17. Epub 2019 Apr 17.

Programa de pós-graduação em Biotecnologia da Universidade Estadual de Feira de Santana, Feira de Santana, BA. Brazil.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2174/1389203720666190417120758DOI Listing
April 2019

Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.

J Med Chem 2019 Feb 6;62(4):1971-1988. Epub 2019 Feb 6.

Department of Chemistry and Chemical Biology, Purdue School of Science , Indiana University-Purdue University Indianapolis , Indianapolis , Indiana 46202 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jmedchem.8b01529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6583781PMC
February 2019

Cryptic binding sites on proteins: definition, detection, and druggability.

Curr Opin Chem Biol 2018 06 23;44:1-8. Epub 2018 May 23.

Department of Chemistry, Boston University, Boston, MA 02215, United States. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S13675931183005
Publisher Site
http://dx.doi.org/10.1016/j.cbpa.2018.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6088748PMC
June 2018

Exploring the structural origins of cryptic sites on proteins.

Proc Natl Acad Sci U S A 2018 04 26;115(15):E3416-E3425. Epub 2018 Mar 26.

Department of Biomedical Engineering, Boston University, Boston, MA 02215;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1711490115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5899430PMC
April 2018

New additions to the ClusPro server motivated by CAPRI.

Proteins 2017 03 5;85(3):435-444. Epub 2017 Jan 5.

Department of Applied Mathematics and Statistics, Stony Brook University, New York.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.25219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313348PMC
March 2017

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking.

J Mol Biol 2017 02 19;429(3):372-381. Epub 2016 Oct 19.

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2016.10.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538892PMC
February 2017

The ClusPro web server for protein-protein docking.

Nat Protoc 2017 Feb 12;12(2):255-278. Epub 2017 Jan 12.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nprot.2016.169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540229PMC
February 2017

A benchmark testing ground for integrating homology modeling and protein docking.

Proteins 2017 01 13;85(1):10-16. Epub 2016 Nov 13.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.25063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5817996PMC
January 2017

Accounting for pairwise distance restraints in FFT-based protein-protein docking.

Bioinformatics 2016 11 29;32(21):3342-3344. Epub 2016 Jun 29.

Department of Applied Mathematics and Statistics Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095118PMC
November 2016

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Authors:
Marc F Lensink Sameer Velankar Andriy Kryshtafovych Shen-You Huang Dina Schneidman-Duhovny Andrej Sali Joan Segura Narcis Fernandez-Fuentes Shruthi Viswanath Ron Elber Sergei Grudinin Petr Popov Emilie Neveu Hasup Lee Minkyung Baek Sangwoo Park Lim Heo Gyu Rie Lee Chaok Seok Sanbo Qin Huan-Xiang Zhou David W Ritchie Bernard Maigret Marie-Dominique Devignes Anisah Ghoorah Mieczyslaw Torchala Raphaël A G Chaleil Paul A Bates Efrat Ben-Zeev Miriam Eisenstein Surendra S Negi Zhiping Weng Thom Vreven Brian G Pierce Tyler M Borrman Jinchao Yu Françoise Ochsenbein Raphaël Guerois Anna Vangone João P G L M Rodrigues Gydo van Zundert Mehdi Nellen Li Xue Ezgi Karaca Adrien S J Melquiond Koen Visscher Panagiotis L Kastritis Alexandre M J J Bonvin Xianjin Xu Liming Qiu Chengfei Yan Jilong Li Zhiwei Ma Jianlin Cheng Xiaoqin Zou Yang Shen Lenna X Peterson Hyung-Rae Kim Amit Roy Xusi Han Juan Esquivel-Rodriguez Daisuke Kihara Xiaofeng Yu Neil J Bruce Jonathan C Fuller Rebecca C Wade Ivan Anishchenko Petras J Kundrotas Ilya A Vakser Kenichiro Imai Kazunori Yamada Toshiyuki Oda Tsukasa Nakamura Kentaro Tomii Chiara Pallara Miguel Romero-Durana Brian Jiménez-García Iain H Moal Juan Férnandez-Recio Jong Young Joung Jong Yun Kim Keehyoung Joo Jooyoung Lee Dima Kozakov Sandor Vajda Scott Mottarella David R Hall Dmitri Beglov Artem Mamonov Bing Xia Tanggis Bohnuud Carlos A Del Carpio Eichiro Ichiishi Nicholas Marze Daisuke Kuroda Shourya S Roy Burman Jeffrey J Gray Edrisse Chermak Luigi Cavallo Romina Oliva Andrey Tovchigrechko Shoshana J Wodak

Proteins 2016 09 1;84 Suppl 1:323-48. Epub 2016 Jun 1.

Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.25007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136PMC
September 2016

Challenges in structural approaches to cell modeling.

J Mol Biol 2016 07 30;428(15):2943-64. Epub 2016 May 30.

Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2016.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976022PMC
July 2016

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.

Proc Natl Acad Sci U S A 2016 07 13;113(30):E4286-93. Epub 2016 Jul 13.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794; Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY 11794

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1603929113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968711PMC
July 2016

Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs.

Drug Discov Today 2016 05 15;21(5):712-7. Epub 2016 Feb 15.

Department of Chemistry, Boston University, Boston, MA, USA; Departments of Biomedical Engineering and Chemistry, Boston University, Boston, MA, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.drudis.2016.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821503PMC
May 2016

Focused grid-based resampling for protein docking and mapping.

J Comput Chem 2016 Apr 2;37(11):961-70. Epub 2016 Feb 2.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.24273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4814242PMC
April 2016

New Frontiers in Druggability.

J Med Chem 2015 Dec 11;58(23):9063-88. Epub 2015 Aug 11.

Acpharis Inc. , Holliston, Massachusetts 01746, United States.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.jmedchem.5b00586
Publisher Site
http://dx.doi.org/10.1021/acs.jmedchem.5b00586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762776PMC
December 2015

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core.

Biochemistry 2015 Dec 4;54(50):7326-34. Epub 2015 Dec 4.

Departments of Chemistry and Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.biochem.5b01086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483379PMC
December 2015

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.

Trends Pharmacol Sci 2015 Nov 1;36(11):724-736. Epub 2015 Nov 1.

Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA; Department of Chemistry, Boston University, Boston, MA, 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tips.2015.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640985PMC
November 2015

Fragments and hot spots in drug discovery.

Oncotarget 2015 Aug;6(22):18740-1

Department of Biomedical Engineering, Boston University, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://www.oncotarget.com/fulltext/4968
Publisher Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662450PMC
http://dx.doi.org/10.18632/oncotarget.4968DOI Listing
August 2015

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro.

J Comput Chem 2015 Jul 10;36(20):1568-72. Epub 2015 Jun 10.

Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.23952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485579PMC
July 2015

Ligand deconstruction: Why some fragment binding positions are conserved and others are not.

Proc Natl Acad Sci U S A 2015 May 27;112(20):E2585-94. Epub 2015 Apr 27.

Department of Biomedical Engineering, Boston University, Boston, MA 02215; Department of Chemistry, Boston University, Boston, MA 02215

View Article

Download full-text PDF

Source
http://www.pnas.org/content/112/20/E2585.full.pdf
Web Search
http://www.pnas.org/lookup/doi/10.1073/pnas.1501567112
Publisher Site
http://dx.doi.org/10.1073/pnas.1501567112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443342PMC
May 2015

The impact of side-chain packing on protein docking refinement.

J Chem Inf Model 2015 Apr 24;55(4):872-81. Epub 2015 Mar 24.

†Division of Systems Engineering, ‡Center for Information and Systems Engineering, §Department of Biomedical Engineering, ∥Department of Mechanical Engineering, and ⊥Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci500380aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734134PMC
April 2015

Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach.

Proc IEEE Conf Decis Control 2014 Dec;2014:5825-5830

D. Kozakov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/CDC.2014.7040301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357846PMC
December 2014

Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro.

Environ Health Perspect 2014 Nov 25;122(11):1225-32. Epub 2014 Jul 25.

Department of Environmental Health, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1289/ehp.1408111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216168PMC
November 2014

In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo.

Mol Pharmacol 2014 Nov 26;86(5):593-608. Epub 2014 Aug 26.

Molecular Medicine Program, Boston University School of Medicine, Boston, Massachusetts (A.J.P., E.A.S., O.N.); Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts (A.J.P., E.A.S., O.N., S.N., J.J.S., DHS); Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts (M.P.P., T.G.H.); Department of Chemistry, Boston University (T.D.A.); Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts (M.E.H., D.G.F.); Wake Forest Innovations, Wake Forest University, Winston-Salem, North Carolina (S.E.H.); and Biomedical Engineering, Boston University, Boston, Massachusetts (D.K., D.B., S.V.)

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1124/mol.114.093369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201140PMC
November 2014

Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces.

PLoS Comput Biol 2014 Oct 2;10(10):e1003872. Epub 2014 Oct 2.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America; Department of Chemistry, Boston University, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1003872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183424PMC
October 2014

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations.

J Chem Theory Comput 2014 Oct 5;10(10):4449-4454. Epub 2014 Sep 5.

Department of Mechanical Engineering, Division of Systems Engineering, and Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ct400474wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196749PMC
October 2014

How proteins bind macrocycles.

Nat Chem Biol 2014 Sep 20;10(9):723-31. Epub 2014 Jul 20.

Department of Chemistry, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio.1584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417626PMC
September 2014

Docking server for the identification of heparin binding sites on proteins.

J Chem Inf Model 2014 Jul 10;54(7):2068-78. Epub 2014 Jul 10.

Program in Bioinformatics and ‡Department of Biomedical Engineering, Boston University , 44 Cummington Street, Boston, Massachusetts 02215, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci500115jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184157PMC
July 2014

Insights into the architecture of the eIF2Bα/β/δ regulatory subcomplex.

Biochemistry 2014 Jun 20;53(21):3432-45. Epub 2014 May 20.

Department of Physiology and Biophysics, Boston University School of Medicine , Boston, Massachusetts 02118, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi500346uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045321PMC
June 2014

How good is automated protein docking?

Proteins 2013 Dec 17;81(12):2159-66. Epub 2013 Oct 17.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.24403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3934018PMC
December 2013

Sampling and scoring: a marriage made in heaven.

Proteins 2013 Nov 19;81(11):1874-84. Epub 2013 Aug 19.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.24343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942495PMC
November 2013

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.

Bioinformatics 2013 May 7;29(9):1218-9. Epub 2013 Mar 7.

Department of Sciences, Wentworth Institute of Technology, Boston, MA 01746, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634182PMC
May 2013

A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy.

PLoS One 2012 11;7(7):e40234. Epub 2012 Jul 11.

Molecular Neurotherapy and Imaging Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040234PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394792PMC
March 2013

Rigid Body Energy Minimization on Manifolds for Molecular Docking.

J Chem Theory Comput 2012 Nov 21;8(11):4374-4380. Epub 2012 Aug 21.

Division of Systems Engineering, Department of Biomedical Engineering, Department of Electrical and Computer Engineering, and Department of Mechanical Engineering, Boston University, Boston, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ct300272jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561712PMC
November 2012

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.

J Chem Inf Model 2012 Aug 24;52(8):2236-44. Epub 2012 Jul 24.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci300175uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623692PMC
August 2012

FTMAP: extended protein mapping with user-selected probe molecules.

Nucleic Acids Res 2012 Jul 15;40(Web Server issue):W271-5. Epub 2012 May 15.

Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gks441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394268PMC
July 2012

Analysis of protein binding sites by computational solvent mapping.

Methods Mol Biol 2012 ;819:13-27

Department of Biomedical Engineering, Biomolecular Engineering Research Center, Boston University, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://structure.bu.edu/sites/default/files/mapping_mmb.pdf
Web Search
http://link.springer.com/10.1007/978-1-61779-465-0_2
Publisher Site
http://dx.doi.org/10.1007/978-1-61779-465-0_2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526383PMC
April 2012

Minimal ensembles of side chain conformers for modeling protein-protein interactions.

Proteins 2012 Feb 22;80(2):591-601. Epub 2011 Nov 22.

BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts; Department of Biomedical Engineering, Boston University, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.23222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297704PMC
February 2012

FTSite: high accuracy detection of ligand binding sites on unbound protein structures.

Bioinformatics 2012 Jan 22;28(2):286-7. Epub 2011 Nov 22.

Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btr651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259439PMC
January 2012

Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery.

J Chem Inf Model 2012 Jan 15;52(1):199-209. Epub 2011 Dec 15.

Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci200468pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264775PMC
January 2012

Analysis of binding site hot spots on the surface of Ras GTPase.

J Mol Biol 2011 Nov 16;413(4):773-89. Epub 2011 Sep 16.

Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2011.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3247908PMC
November 2011

Structural conservation of druggable hot spots in protein-protein interfaces.

Proc Natl Acad Sci U S A 2011 Aug 1;108(33):13528-33. Epub 2011 Aug 1.

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1101835108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158149PMC
August 2011

Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication.

J Virol 2011 Jul 20;85(13):6381-9. Epub 2011 Apr 20.

McIntyre Medical Sciences Building, Rm. 810, 3655 Promenade Sir William Osler, McGill University, Montreal, Quebec, Canada H3G 1Y6.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00078-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126520PMC
July 2011

Where does amantadine bind to the influenza virus M2 proton channel?

Trends Biochem Sci 2010 Sep 8;35(9):471-5. Epub 2010 Apr 8.

Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tibs.2010.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919587PMC
September 2010

Domain motion and interdomain hot spots in a multidomain enzyme.

Protein Sci 2010 Sep;19(9):1662-72

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pro.446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975130PMC
September 2010

The structural basis of pregnane X receptor binding promiscuity.

Biochemistry 2009 Dec;48(48):11572-81

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi901578nDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789303PMC
December 2009

Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel.

Biophys J 2009 Nov;97(10):2846-53

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2009.09.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776279PMC
November 2009

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase.

J Comput Aided Mol Des 2009 Aug 12;23(8):491-500. Epub 2009 Jun 12.

Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, 415 South Street MS 029, Waltham, MA 02454, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10822-009-9283-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889209PMC
August 2009

Convergence and combination of methods in protein-protein docking.

Curr Opin Struct Biol 2009 Apr 25;19(2):164-70. Epub 2009 Mar 25.

Biomolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S0959440X0900028
Publisher Site
http://dx.doi.org/10.1016/j.sbi.2009.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763924PMC
April 2009

DARS (Decoys As the Reference State) potentials for protein-protein docking.

Biophys J 2008 Nov 1;95(9):4217-27. Epub 2008 Aug 1.

Department of Biomedical Engineering, and Program in Bioinformatics, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1529/biophysj.108.135814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567923PMC
November 2008

Protein docking by the underestimation of free energy funnels in the space of encounter complexes.

PLoS Comput Biol 2008 Oct 10;4(10):e1000191. Epub 2008 Oct 10.

Department of Biomedical Engineering, BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1000191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538569PMC
October 2008

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.

Bioinformatics 2008 Sep 30;24(17):1865-73. Epub 2008 Jun 30.

Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btn334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732220PMC
September 2008

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.

Proteins 2008 Aug;72(3):993-1004

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/prot.21997
Publisher Site
http://dx.doi.org/10.1002/prot.21997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823634PMC
August 2008

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.

Conf Proc IEEE Eng Med Biol Soc 2006 ;1:5330-3

Center for Information & Systems Eng., and Dept. of Manufacturing Eng., Boston University, Blookline, MA 2446, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/IEMBS.2006.260790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2446401PMC
March 2008

Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.

Proteins 2007 Dec;69(4):734-42

BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.21754DOI Listing
December 2007

ClusPro: performance in CAPRI rounds 6-11 and the new server.

Proteins 2007 Dec;69(4):781-5

Dyax Corp., Cambridge, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.21795DOI Listing
December 2007

Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10.

Biochemistry 2007 Aug 24;46(32):9239-49. Epub 2007 Jul 24.

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi700336yDOI Listing
August 2007

Computational methods for functional site identification suggest a substrate access channel in transaldolase.

Genome Inform 2006 ;17(1):13-22

Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
July 2007

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.

IEEE Trans Automat Contr 2007 Apr;52(4):664-676

Center for Information and Systems Engineering, and Department of Manufacturing Engineering, and the Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215 USA (e-mail: ).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/TAC.2007.894518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744142PMC
April 2007

Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs.

Biochemistry 2007 Mar 15;46(10):2640-54. Epub 2007 Feb 15.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi062320mDOI Listing
March 2007

Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.

J Med Chem 2007 Mar 17;50(6):1231-40. Epub 2007 Feb 17.

Bioinformatics Graduate Program, Boston University, 24 Cummington Street, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jm061134bDOI Listing
March 2007

Engineering a novel, stable dimeric streptavidin with lower isoelectric point.

J Biotechnol 2007 Feb 26;128(2):213-25. Epub 2006 Sep 26.

Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jbiotec.2006.08.014DOI Listing
February 2007

PIPER: an FFT-based protein docking program with pairwise potentials.

Proteins 2006 Nov;65(2):392-406

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.21117DOI Listing
November 2006

Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.

Biochemistry 2006 Aug;45(31):9393-407

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi060343vDOI Listing
August 2006

Computational screening of phthalate monoesters for binding to PPARgamma.

Chem Res Toxicol 2006 Aug;19(8):999-1009

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/tx050301sDOI Listing
August 2006

Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.

J Mol Graph Model 2006 May 10;24(6):426-33. Epub 2005 Oct 10.

Graduate Program in Bioinformatics and Systems Biology, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2005.08.004DOI Listing
May 2006

Characterization of protein-ligand interaction sites using experimental and computational methods.

Curr Opin Drug Discov Devel 2006 May;9(3):354-62

Department of Biomedical Engineering, Boston University and SolMap Pharmaceuticals, 44 Cummington Street, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
May 2006

Optimal clustering for detecting near-native conformations in protein docking.

Biophys J 2005 Aug 20;89(2):867-75. Epub 2005 May 20.

Department of Biomedical Engineering, Boston University, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1529/biophysj.104.058768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366636PMC
August 2005

Classification of protein complexes based on docking difficulty.

Authors:
Sandor Vajda

Proteins 2005 Aug;60(2):176-80

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.20554DOI Listing
August 2005

Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.

Proteins 2005 Aug;60(2):239-44

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.20564DOI Listing
August 2005