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Dmitry Kondrashov
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Year
Ensemble refinement of protein crystal structures: validation and application
EJ Levin, DA Kondrashov, GE Wesenberg, GN Phillips
Structure 15 (9), 1040-1052, 2007
2002007
Protein structural variation in computational models and crystallographic data
DA Kondrashov, AW Van Wynsberghe, RM Bannen, Q Cui, GN Phillips
Structure 15 (2), 169-177, 2007
1262007
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data
DA Kondrashov, Q Cui, GN Phillips
Biophysical journal 91 (8), 2760-2767, 2006
1262006
Topological features of rugged fitness landscapes in sequence space
DA Kondrashov, FA Kondrashov
Trends in Genetics 31 (1), 24-33, 2015
1042015
Protein Functional Cycle Viewed at Atomic Resolution:  Conformational Change and Mobility in Nitrophorin 4 as a Function of pH and NO Binding,
DA Kondrashov, SA Roberts, A Weichsel, WR Montfort
Biochemistry 43 (43), 13637-13647, 2004
752004
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
DA Kondrashov, W Zhang, R Aranda IV, B Stec, GN Phillips Jr
Proteins: Structure, Function, and Bioinformatics 70 (2), 353-362, 2008
582008
Structure and Dynamics of UDP–Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP–Glucose and UTP
JG McCoy, E Bitto, CA Bingman, GE Wesenberg, RM Bannen, ...
Journal of molecular biology 366 (3), 830-841, 2007
572007
Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain
E Bitto, CA Bingman, L Bittova, DA Kondrashov, RM Bannen, BG Fox, ...
Journal of biological chemistry 283 (44), 30184-30192, 2008
462008
Creating protein models from electron-density maps using particle-filtering methods
F DiMaio, DA Kondrashov, E Bitto, A Soni, CA Bingman, GN Phillips Jr, ...
Bioinformatics 23 (21), 2851-2858, 2007
382007
Nonequilibrium dynamics simulations of nitric oxide release: comparative study of nitrophorin and myoglobin
DA Kondrashov, WR Montfort
The Journal of Physical Chemistry B 111 (31), 9244-9252, 2007
262007
Structure and dynamics of γ‐SNAP: Insight into flexibility of proteins from the SNAP family
E Bitto, CA Bingman, DA Kondrashov, JG McCoy, RM Bannen, ...
Proteins: Structure, Function, and Bioinformatics 70 (1), 93-104, 2008
212008
Quantifying life: A symbiosis of computation, mathematics, and biology
DA Kondrashov
University of Chicago Press, 2020
32020
Using normal mode analysis in teaching mathematical modeling to biology students
DA Kondrashov
Mathematical Modelling of Natural Phenomena 6 (6), 278-294, 2011
22011
Molecular mastication mechanics
DA Kondrashov, GN Phillips
Structure 13 (6), 836-837, 2005
22005
Geometric Theory of Crystal Growth
D KONDRASHOV
11998
MSIS-Kondrashov: Effect of alternative assessment modalities on student satisfaction and learning in quantitative biology
D Kondrashov
2023
Comparison of assessment and teaching modalities for a quantitative biology course
D Kondrashov
2022
Teaching Quantitative Modeling Remotely
D Kondrashov
2020
Teaching Data Analysis Using Students' Own Data
D Kondrashov, S Allesina
2019
Discrete stochastic modeling for first-year biology students
D Kondrashov
2017
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Articles 1–20