Abdallah Sayyed-Ahmad

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Alemayehu (Alex) GorfeProfessor, University of Texas McGovern Medical School-HoustonVerified email at uth.tmc.edu
Priyanka PrakashMcGovern Medical School, University of Texas Health Science Center at HoustonVerified email at uth.tmc.edu
Yiannis N. KaznessisGeneral Probiotics Inc.Verified email at gprobiotics.com
Kagan TuncayDepartment of Civil Engineering, Middle East Technical University, Ankara, TurkeyVerified email at metu.edu.tr
John F HancockUniversity of Texas Medial School at HoustonVerified email at uth.tmc.edu
Dan BolintineanuSandia National LaboratoriesVerified email at sandia.gov
Birgit StrodelProfessor, Computational Biochemistry, Research Centre Jülich & University Düsseldorf, GermanyVerified email at strodel.info
Mohammed KhaledPhD candidate, IBI-7 Forschungszentrum JülichVerified email at fz-juelich.de
Barry GrantUniversity of California, San DiegoVerified email at ucsd.edu
L M LichtenbergerVerified email at uth.edu
David E. VolkUniversity of Texas Health Science CenterVerified email at uth.tmc.edu
David G. GorensteinUniversity of Texas USC Houston (retired)Verified email at am-biotech.com
Yong ZhouUniversity of Texas Health Science CenterVerified email at uth.tmc.edu
Yves V. BrunProfessor and Canada 150 Research Chair at the Université de MontréalVerified email at umontreal.ca
Khuloud JaqamanAssistant Professor, Dept of Biophysics and Lyda Hill Dept of Bioinformatics, UT SouthwesternVerified email at utsouthwestern.edu
Ali NavidStaff Scientist, Lawrence Livermore National LaboratoryVerified email at llnl.gov
himanshu khandeliaUniversity of Southern Denmark Verified email at sdu.dk
Yinglong MiaoUniversity of KansasVerified email at ku.edu
Dong-Hoon SheenProfessor, Chonnam National UniversityVerified email at jnu.ac.kr
John RuppIndiana UniversityVerified email at indiana.edu

Abdallah Sayyed-Ahmad

Professor of Physics, Birzeit University

Verified email at birzeit.edu - Homepage

Molecular Modelling Molecular Dynamics Free Energy Calculations Computational Biophysics


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Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers P Prakash, A Sayyed-Ahmad, KJ Cho, DM Dolino, W Chen, H Li, BJ Grant, ... Scientific reports 7 (1), 1-11, 2017	92	2017
Spatiotemporal analysis of K-Ras plasma membrane interactions reveals multiple high order homo-oligomeric complexes S Sarkar-Banerjee, A Sayyed-Ahmad, P Prakash, KJ Cho, MN Waxham, ... Journal of the American Chemical Society 139 (38), 13466-13475, 2017	72	2017
On the nature of antimicrobial activity: a model for protegrin-1 pores AA Langham, AS Ahmad, YN Kaznessis Journal of the American Chemical Society 130 (13), 4338-4346, 2008	71	2008
Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore DS Bolintineanu, A Sayyed-Ahmad, HT Davis, YN Kaznessis PLoS computational biology 5 (1), e1000277, 2009	65	2009
The role of conserved waters in conformational transitions of Q61H K-ras P Prakash, A Sayyed-Ahmad, AA Gorfe PLoS computational biology 8 (2), e1002394, 2012	52	2012
Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane H Fatafta, M Khaled, MC Owen, A Sayyed-Ahmad, B Strodel Proceedings of the National Academy of Sciences 118 (39), e2106210118, 2021	46	2021
Distinct dynamics and interaction patterns in H‐and K‐Ras oncogenic P‐loop mutants A Sayyed‐Ahmad, P Prakash, AA Gorfe Proteins: Structure, Function, and Bioinformatics 85 (9), 1618–1632, 2017	44	2017
Efficient solution technique for solving the Poisson–Boltzmann equation A Sayyed–Ahmad, K Tuncay, PJ Ortoleva Journal of computational chemistry 25 (8), 1068-1074, 2004	44	2004
Computational equilibrium thermodynamic and kinetic analysis of K-Ras dimerization through an effector binding surface suggests limited functional role A Sayyed-Ahmad, KJ Cho, JF Hancock, AA Gorfe The Journal of Physical Chemistry B 120 (33), 8547-8556, 2016	41	2016
Structure and dynamics of cholic acid and dodecylphosphocholine− cholic acid aggregates A Sayyed-Ahmad, LM Lichtenberger, AA Gorfe Langmuir 26 (16), 13407-13414, 2010	37	2010
pMD-membrane: a method for ligand binding site identification in membrane-bound proteins P Prakash, A Sayyed-Ahmad, AA Gorfe PLoS computational biology 11 (10), e1004469, 2015	35	2015
Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles P Prakash, A Sayyed-Ahmad, Y Zhou, DE Volk, DG Gorenstein, E Dial, ... Biochimica et Biophysica Acta (BBA)-Biomembranes 1818 (12), 3040-3047, 2012	33	2012
Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory A Sayyed-Ahmad, K Tuncay, PJ Ortoleva BMC bioinformatics 8 (1), 1-18, 2007	32	2007
The Karyote^® Physico-Chemical Genomic, Proteomic, Metabolic Cell Modeling System P Ortoleva, E Berry, Y Brun, J Fan, M Fontus, K Hubbard, K Jaqaman, ... OMICS A Journal of Integrative Biology 7 (3), 269-283, 2003	25	2003
Conformational and dynamical effects of Tyr32 phosphorylation in K-Ras: molecular dynamics simulation and Markov state models analysis M Khaled, A Gorfe, A Sayyed-Ahmad The Journal of Physical Chemistry B 123 (36), 7667-7675, 2019	23	2019
Mixed-probe simulation and probe-derived surface topography map analysis for ligand binding site identification A Sayyed-Ahmad, AA Gorfe Journal of chemical theory and computation 13 (4), 1851-1861, 2017	21	2017
Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model A Sayyed-Ahmad, YN Kaznessis PLoS One 4 (3), e4799, 2009	20	2009
Toward automated cell model development through information theory A Sayyed-Ahmad, K Tuncay, PJ Ortoleva The Journal of Physical Chemistry A 107 (49), 10554-10565, 2003	17	2003
Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles A Sayyed-Ahmad, H Khandelia, YN Kaznessis Molecular simulation 35 (10-11), 986-997, 2009	16	2009
Design of an optical water pollution sensor using a single-layer guided-mode resonance filter E Sader, A Sayyed-Ahmad Photonic Sensors 3, 224-230, 2013	15	2013

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