John L. Klepeis

16.3k citations

33 papers · 10.6k indexed · 4 hit papers · h-index 24

Molecular Biology top 0.5%
Materials Chemistry top 2%
Computational Theory and Mathematics top 0.1%
Organic Chemistry top 2%
Spectroscopy top 1%

Co-authors: David E. Shaw Ron O. Dror Kresten Lindorff‐Larsen Stefano Piana Paul Maragakis Kim Palmö Michael P. Eastwood Yibing Shan
Topics: Protein Structure and Dynamics (17 papers)Enzyme Structure and Function (8 papers)Advanced Chemical Physics Studies (6 papers)
Cited by: Computational Theory and Mathematics Molecular Biology Numerical Analysis
Journals: Science Journal of the American Chemical Society The Journal of Chemical Physics
Partner nations: United States Germany

In The Last Decade

John L. Klepeis

33 papers receiving 10.5k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

2010 4.7k citations Kresten Lindorff‐Larsen, Stefano Piana et al. Proteins Structure Function and Bioinformatics profile →
Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters

2006 1.9k citations K. J. Bowers, Federico D. Sacerdoti et al. profile →
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

2006 1.2k citations K. J. Bowers, Huafeng Xu et al. profile →
Long-timescale molecular dynamics simulations of protein structure and function

2009 578 citations John L. Klepeis, Kresten Lindorff‐Larsen et al. Current Opinion in Structural Biology profile →

Peers

Countries citing papers authored by John L. Klepeis

Since Specialization

Citations

This map shows the geographic impact of John L. Klepeis's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by John L. Klepeis with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites John L. Klepeis more than expected).

Fields of papers citing papers by John L. Klepeis

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by John L. Klepeis. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by John L. Klepeis. The network helps show where John L. Klepeis may publish in the future.

Co-authorship network of co-authors of John L. Klepeis

This figure shows the co-authorship network connecting the top 25 collaborators of John L. Klepeis. A scholar is included among the top collaborators of John L. Klepeis based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with John L. Klepeis. John L. Klepeis is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work	Indexed citations
1	Accurate parameterization of the kinetic energy functional for calculations using exact-exchange 2021 ·The Journal of Chemical Physics ·(unknown),Babak Sadigh,Siya Zhu,Phanish Suryanarayana,(unknown),Brian Gallagher,Vasily V. Bulatov,John L. Klepeis,Amit Samanta	4
2	Quantum chemical benchmark databases of gold-standard dimer interaction energies 2021 ·Scientific Data ·Alexander Donchev,Andrew G. Taube,(unknown),Cory Hargus,Robert T. McGibbon,(unknown),Brent A. Gregersen,Je-Luen Li,Kim Palmö,Karthik Siva,Michael Bergdorf,John L. Klepeis,David E. Shaw	69
3	Improving the accuracy of Møller-Plesset perturbation theory with neural networks 2017 ·The Journal of Chemical Physics ·Robert T. McGibbon,Andrew G. Taube,Alexander Donchev,Karthik Siva,Felipe Hernández,Cory Hargus,(unknown),John L. Klepeis,David E. Shaw	82
4	Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations 2014 ·Current Opinion in Structural Biology ·Stefano Piana,John L. Klepeis,David E. Shaw	374
5	Improved side‐chain torsion potentials for the Amber ff99SB protein force fieldbreakdown → 2010 ·Proteins Structure Function and Bioinformatics ·Kresten Lindorff‐Larsen,Stefano Piana,Kim Palmö,Paul Maragakis,John L. Klepeis,Ron O. Dror,David E. Shaw	4652
6	Long-timescale molecular dynamics simulations of protein structure and functionbreakdown → 2009 ·Current Opinion in Structural Biology ·John L. Klepeis,Kresten Lindorff‐Larsen,Ron O. Dror,David E. Shaw	578
7	A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories 2008 ·IEEE International Conference on High Performance Computing, Data, and Analytics ·Tiankai Tu,Charles A. Rendleman,David W. Borhani,Ron O. Dror,Justin Gullingsrud,Morten Ø. Jensen,John L. Klepeis,Paul Maragakis,Patrick J. O. Miller,Kate A. Stafford,David E. Shaw	36
8	High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation 2008 ·Richard H. Larson,John K. Salmon,Ron O. Dror,Martin M. Deneroff,Cliff Young,J.P. Grossman,Yibing Shan,John L. Klepeis,(unknown)	15
9	Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins 2008 ·The Journal of Physical Chemistry B ·Paul Maragakis,Kresten Lindorff‐Larsen,Michael P. Eastwood,Ron O. Dror,John L. Klepeis,Isaiah T. Arkin,Morten Ø. Jensen,Huafeng Xu,Nikola Trbovic,Richard A. Friesner,Arthur G. Palmer,David E. Shaw	163
10	Mechanism of Na ⁺ /H ⁺ Antiporting 2007 ·Science ·Isaiah T. Arkin,Huafeng Xu,Morten Ø. Jensen,Eyal Arbely,Estelle R. Bennett,K. J. Bowers,Edmond Chow,Ron O. Dror,Michael P. Eastwood,(unknown),Brent A. Gregersen,John L. Klepeis,István Kolossváry,Yibing Shan,David E. Shaw	124
11	Novel approach for α‐helical topology prediction in globular proteins: Generation of interhelical restraints 2006 ·Proteins Structure Function and Bioinformatics ·S. R. McAllister,(unknown),John L. Klepeis,Christodoulos A. Floudas	15
12	Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clustersbreakdown → 2006 ·K. J. Bowers,Federico D. Sacerdoti,John K. Salmon,Yibing Shan,David E. Shaw,Edmond Chow,Huafeng Xu,Ron O. Dror,Michael P. Eastwood,Brent A. Gregersen,John L. Klepeis,István Kolossváry,Mark A. Moraes	1925
13	Gaussian split Ewald: A fast Ewald mesh method for molecular simulation 2005 ·The Journal of Chemical Physics ·Yibing Shan,John L. Klepeis,Michael P. Eastwood,Ron O. Dror,David E. Shaw	323
14	Ab initio prediction of the three‐dimensional structure of a de novo designed protein: A double‐blind case study 2004 ·Proteins Structure Function and Bioinformatics ·John L. Klepeis,Yinan Wei,Michael H. Hecht,Christodoulos A. Floudas	44
15	Design of Peptide Analogues with Improved Activity Using a Novel de Novo Protein Design Approach 2004 ·Industrial & Engineering Chemistry Research ·John L. Klepeis,Christodoulos A. Floudas,Dimitrios Morikis,(unknown),John D. Lambris	44
16	ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence 2003 ·Biophysical Journal ·John L. Klepeis,Christodoulos A. Floudas	92
17	A new pairwise folding potential based on improved decoy generation and side‐chain packing 2003 ·Proteins Structure Function and Bioinformatics ·(unknown),John L. Klepeis,Christodoulos A. Floudas	36
18	Hybrid Global Optimization Algorithms for Protein Structure Prediction: Alternating Hybrids 2003 ·Biophysical Journal ·John L. Klepeis,(unknown),Christodoulos A. Floudas	53
19	Ab initio Tertiary Structure Prediction of Proteins 2003 ·Journal of Global Optimization ·John L. Klepeis,Christodoulos A. Floudas	44
20	Protein folding and peptide docking: A molecular modeling and global optimization approach 1998 ·Computers & Chemical Engineering ·John L. Klepeis,Marianthi Ierapetritou,Christodoulos A. Floudas	12

About John L. Klepeis

John L. Klepeis is a scholar working on Hardware and Architecture, Spectroscopy and Molecular Biology, having authored 33 papers that have together received 10.6k indexed citations. Recurring topics across this work include Protein Structure and Dynamics (17 papers), Enzyme Structure and Function (8 papers) and Advanced Chemical Physics Studies (6 papers). The work is most often cited by research in Computational Theory and Mathematics (1.8k citations), Molecular Biology (7.0k citations) and Numerical Analysis (303 citations). John L. Klepeis has collaborated with scholars based in United States and Germany. Frequent co-authors include David E. Shaw, Ron O. Dror, Kresten Lindorff‐Larsen, Stefano Piana, Paul Maragakis, Kim Palmö, Michael P. Eastwood, Yibing Shan, Huafeng Xu and Brent A. Gregersen. Their work appears in journals such as Science, Journal of the American Chemical Society and The Journal of Chemical Physics.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

Explore authors with similar magnitude of impact